10x Genomics Support/Cell Ranger/Release Notes/

Reference Release Notes

Instructions for building the 10x Genomics Public Reference are documented separately.

Build Steps

2024-A reference packages are not backward compatible with Cell Ranger v5.0.1 and prior.

  • Human GRCh38 (GENCODE v44/Ensembl110 annotations)
  • Mouse GRCm39 (GENCODE vM33/Ensembl110 annotations)
  • Human and mouse GRCh38 and GRCm39

Update notes:

  • Human transcriptome annotations have been updated from GENCODE v32 to GENCODE v44.
  • Mouse transcriptome annotations have been updated from vM23 to vM33.
  • Readthrough annotations have been improved, and erroneous systematic gene names have been removed.
  • Polymorphic pseudogenes were included by adding protein_coding_LoF to the list of accepted biotypes.
  • Pseudoautosomal regions (PAR) on the Y chromosome have been masked and the pseudoautosomal genes on the Y chromosome have been removed from the GTF. The corresponding genes on the X chromosome are still present in the GTF and will have associated counts.
  • Summary of changes is shown in the table:
Number of new gene IDs23391746
Number of genes removed301335
Number of gene names changed129131905
Number of gene IDs changed (based on gene name)6956
  • List of affected human and mouse genes are available for download.

2020-A reference packages are backward compatible with Cell Ranger v3.1.0 and prior.

Human GRCh38 (GENCODE v32/Ensembl98)

Mouse mm10 (GENCODE vM23/Ensembl98)

Human and mouse GRCh38 and mm10

Update notes:

  • Transcriptome annotations updated from Ensembl 93 to GENCODE v32 (human) and vM23 (mouse), which are equivalent to Ensembl 98.
  • GRCh38 and mm10 sequences are not changed; chromosome names now follow the GENCODE/UCSC convention (e.g., chr1 and chrM) rather than the Ensembl convention (1 and MT).
  • Additional filtering removes genes with unreliable annotations that often overlap more legitimate genes (see build scripts for details), resulting in improved overall sensitivity.
  • Mapping rates and gene/UMI sensitivity are increased due to more comprehensive annotations and improved manual curation of genes:

Human and mouse 3.1.0 GRCh38 and mm10

Human 3.0.0 GRCh38 Human 3.0.0 hg19 Mouse 3.0.0 mm10 Human and mouse 3.0.0 hg19 and mm10

Mouse mm10 (V(D)J genes included) Human and house hg19 and mm10 (with V(D)J)

Human 1.2.0 GRCh38 Human 1.2.0 hg19 Mouse 1.2.0 mm10 Human and mouse 1.2.0 hg19 and mm10 ERCC reference ercc92

Human V(D)J reference GRCh38

The Human V(D)J reference has been updated to exclude the following genes:

  • IGHV4-30-2
  • IGKV1D-33
  • IGKV1D-37
  • IGKV1D-39
  • IGKV2D-28

These genes have counterparts with identical V, D, J, and C gene sequences, but differ in the length of their 5' UTRs. Removing duplicates improves clonotype assignment.

  • Added human gene IGHV3-9
  • For two genes that are identical except for extra bases on the 3' end, only the longer version was retained. List of affected genes:


IGHA1 ENST00000390547 IGHD ENST00000390556 IGHD1-1 ENST00000454908 IGHD1-14 ENST00000451044 IGHD1-20 ENST00000450276 IGHD1-26 ENST00000390567 IGHD1-7 ENST00000430425 IGHD1/OR15-1A ENST00000605284 IGHD2-15 ENST00000390578 IGHD2-2 ENST00000390591 IGHD2-21 ENST00000390572 IGHD2-8 ENST00000390585 IGHD2/OR15-2A ENST00000603077 IGHD3-10 ENST00000390583 IGHD3-16 ENST00000390577 IGHD3-22 ENST00000390571 IGHD3-3 ENST00000390590 IGHD3-9 ENST00000390584 IGHD3/OR15-3A ENST00000604950 IGHD4-11 ENST00000431440 IGHD4-17 ENST00000431870 IGHD4-23 ENST00000437320 IGHD4/OR15-4A ENST00000603326 IGHD5-12 ENST00000390581 IGHD5-18 ENST00000390575 IGHD5-24 ENST00000390569 IGHD5/OR15-5A ENST00000604642 IGHD6-13 ENST00000390580 IGHD6-19 ENST00000390574 IGHD6-25 ENST00000452198 IGHD6-6 ENST00000454691 IGHD7-27 ENST00000439842 IGHG1 ENST00000390542 IGHG1 ENST00000390548 IGHG1 ENST00000390549 IGHG2 ENST00000390545 IGHG3 ENST00000390551 IGHG4 ENST00000390543 IGHJ1 ENST00000390565 IGHM ENST00000390559 IGHV1-18 ENST00000390605 IGHV1-2 ENST00000390594 IGHV1-24 ENST00000390610 IGHV1-3 ENST00000390595 IGHV1-45 ENST00000390621 IGHV1-46 ENST00000390622 IGHV1-58 ENST00000390628 IGHV1-69 ENST00000390633 IGHV1-69-2 ENST00000615784 IGHV2-26 ENST00000390611 IGHV2-5 ENST00000390597 IGHV2-70D ENST00000390634 IGHV3-11 ENST00000390601 IGHV3-13 ENST00000390602 IGHV3-15 ENST00000390603 IGHV3-16 ENST00000390604 IGHV3-20 ENST00000390606 IGHV3-21 ENST00000390607 IGHV3-23 ENST00000390609 IGHV3-30 ENST00000603660 IGHV3-35 ENST00000390617 IGHV3-38 ENST00000390618 IGHV3-43 ENST00000434710 IGHV3-48 ENST00000390624 IGHV3-49 ENST00000390625 IGHV3-53 ENST00000390627 IGHV3-64 ENST00000454421 IGHV3-66 ENST00000390632 IGHV3-7 ENST00000390598 IGHV3-72 ENST00000433072 IGHV3-73 ENST00000390636 IGHV3-74 ENST00000424969 IGHV4-28 ENST00000390612 IGHV4-34 ENST00000390616 IGHV4-39 ENST00000390619 IGHV4-4 ENST00000455737 IGHV4-59 ENST00000390629 IGHV4-61 ENST00000390630 IGHV5-51 ENST00000390626 IGHV6-1 ENST00000390593 IGKV1-12 ENST00000480492 IGKV1-16 ENST00000479981 IGKV1-17 ENST00000490686 IGKV1-27 ENST00000498435 IGKV1-33 ENST00000473726 IGKV1-37 ENST00000465170 IGKV1-39 ENST00000498574 IGKV1-5 ENST00000496168 IGKV1-6 ENST00000464162 IGKV1-8 ENST00000495489 IGKV1-9 ENST00000493819 IGKV2-24 ENST00000484817 IGKV2-28 ENST00000482769 IGKV2-30 ENST00000468494 IGKV3-11 ENST00000483158 IGKV3-15 ENST00000390252 IGKV3-20 ENST00000492167 IGKV3-7 ENST00000390247 IGKV3D-7 ENST00000443397 IGKV5-2 ENST00000390244 IGKV6-21 ENST00000390256 IGLV1-36 ENST00000390301 IGLV1-40 ENST00000390299 IGLV1-44 ENST00000628287 IGLV2-33 ENST00000390302 IGLV3-32 ENST00000390303 IGLV5-37 ENST00000390300 IGLV7-43 ENST00000390298 TRBD1 ENST00000631435 TRBJ1-1 ENST00000634213 TRBJ1-2 ENST00000631745 TRBJ1-3 ENST00000633780 TRBJ1-4 ENST00000632041 TRBJ1-5 ENST00000634000 TRBJ2-1 ENST00000390412 TRBJ2-2 ENST00000390413 TRBJ2-2P ENST00000390414 TRBJ2-3 ENST00000390415 TRBJ2-4 ENST00000390416 TRBJ2-5 ENST00000390417 TRBJ2-6 ENST00000390418 TRBV10-1 ENST00000390364 TRBV11-1 ENST00000390367 TRBV11-3 ENST00000611787 TRBV12-3 ENST00000620569 TRBV13 ENST00000614171 TRBV14 ENST00000617639 TRBV15 ENST00000616518 TRBV16 ENST00000620773 TRBV23-1 ENST00000390396 TRBV27 ENST00000390399 TRBV28 ENST00000390400 TRBV29-1 ENST00000422143 TRBV3-1 ENST00000390387 TRBV4-2 ENST00000390392 TRBV5-1 ENST00000390381 TRBV5-6 ENST00000390375 TRBV5-7 ENST00000390378 TRBV6-1 ENST00000390353 TRBV6-5 ENST00000390368 TRBV7-1 ENST00000547918 TRBV7-7 ENST00000390377 TRGJ1 ENST00000390337


Added missing mouse TRGV and TRGC genes

TRGC1 ENSMUST00000103558 TRGC2 ENSMUST00000103561 TRGC3 ENSMUST00000198163 TRGC4 ENSMUST00000179181 TRGV1 ENSMUST00000103564 TRGV3 ENSMUST00000198663 TRGV4 ENSMUST00000103554 TRGV5 ENSMUST00000199017 TRGV6 ENSMUST00000198330 TRGV7 ENSMUST00000103553

For two genes that are identical except for extra bases on the 3' end, only the longer version was retained. List of affected genes:

IGHD2-5 ENSMUST00000178549 IGHD5-2 ENSMUST00000179166 TRAV11D ENSMUST00000103648 TRAV12D-1 ENSMUST00000181360 TRAV12D-2 ENSMUST00000197007 TRAV13D-2 ENSMUST00000197954 TRAV14D-1 ENSMUST00000181038 TRAV14D-2 ENSMUST00000196802 TRAV15D-2-DV6D-2 ENSMUST00000199800 TRAV3D-3 ENSMUST00000196023 TRAV4D-3 ENSMUST00000103592 TRAV4D-4 ENSMUST00000103600 TRAV5D-4 ENSMUST00000179701 TRAV6-6 ENSMUST00000103584 TRAV7-2 ENSMUST00000103636 TRAV7D-5

The recommended V(D)J reference packages for human and mouse have been updated from v4.0-5.0. The changes to the V(D)J reference sequences are listed below:


Replace IGKV2D-40, whose leader sequence appears to be truncated. Delete IGKV2-18, which is probably a pseudogene. Delete IGLV5-48, which is truncated on the right. Delete TRBV21-1, which has multiple frameshifts. Add IGHV4-30-4, which was missing. Add IGKV1-NL1, which was missing. Add IGHV4-38-2, which was missing.


Delete TRAV23, which is frame-shifted. Delete the first base of the constant region gene IGHG2B. Make a six-base insertion in IGKV12-89, based on empirical data. Correct IGHV8-9, whose amino acid sequence showed the canonical C at the end of FWR3 as S. This is consistent with 10x data. Add an allele of IGKV2-109, which was missing. Add IGKV4-56, which was missing. Add IGHV1-2, which was missing.

Recommended V(D)J reference packages for human and mouse have been updated from version 3.1.0 to 4.0.0. The changes to the V(D)J reference sequences are listed below:

  • Remove the first base of the C region in certain cases. In these cases we observe that in most transcripts, the J region and C region overlap by exactly one base.
  • Add an allele of the gene IGHJ6 to the human V(D)J reference.

Updates to prebuilt reference: https://support.10xgenomics.com/single-cell-vdj/software/pipelines/3.1/advanced/built-in-refs