BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525116.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 617,101 number of mapped reads = 559,935 (90.74%) number of supplementary alignments = 16,044 (2.6%) number of secondary alignments = 0 number of mapped bases = 43,400,183 bp number of sequenced bases = 43,382,650 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 10,711 duplication rate = 1.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3958 >>>>>>> ACTG content number of A's = 11,572,105 bp (26.67%) number of C's = 8,831,566 bp (20.36%) number of T's = 13,040,283 bp (30.06%) number of G's = 9,937,030 bp (22.91%) number of N's = 1,666 bp (0%) GC percentage = 43.26% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 306,864 number of insertions = 3,525 mapped reads with insertion percentage = 0.62% number of deletions = 9,956 mapped reads with deletion percentage = 1.75% homopolymer indels = 44.02% >>>>>>> Coverage mean coverageData = 0.014X std coverageData = 0.1697X There is a 1.32% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3469372 0.013919211057853292 0.24145852631891243 chr2 243199373 3748362 0.015412712433267663 0.22609307141593074 chr3 198022430 2896922 0.01462926194775006 0.1253926774604687 chr4 191154276 2879556 0.015064041779531 0.1305807166246234 chr5 180915260 2654127 0.014670553495597883 0.1269701244203072 chr6 171115067 2529920 0.014784904943525516 0.1363158229750426 chr7 159138663 2384415 0.014983253943763496 0.23733269671222612 chr8 146364022 2281038 0.01558469061474684 0.22669330628824724 chr9 141213431 1807780 0.012801756796065666 0.1638155730806267 chr10 135534747 2024935 0.014940338509651699 0.16839664446581715 chr11 135006516 1962171 0.014533898497165871 0.16447506520774083 chr12 133851895 1997915 0.014926310905049197 0.12707171021066344 chr13 115169878 1366256 0.011862962987596462 0.11260413431087013 chr14 107349540 1300985 0.012119148344743723 0.12040844568256236 chr15 102531392 1246381 0.012156091668003494 0.11397191467881242 chr16 90354753 1228792 0.013599638748389917 0.12585581606095494 chr17 81195210 1128256 0.01389559802850439 0.13678597149548496 chr18 78077248 1168552 0.014966613577363792 0.23964229083663738 chr19 59128983 848939 0.014357409123711801 0.19120228022238495 chr20 63025520 867374 0.013762266459681729 0.12402838219888773 chr21 48129895 568202 0.011805594007632886 0.11618969707500545 chr22 51304566 472647 0.00921257184009704 0.09907603509814294 chrMT 16571 4067 0.24542876108864883 0.482312912431658 chrX 155270560 2449063 0.015772874136603873 0.14998923898704555 chrY 59373566 114156 0.0019226738040292208 0.05617858432507001