BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10174093.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP222840/SRP222840.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 = 4,221,490 number of mapped reads = 4,135,602 (97.97%) number of supplementary alignments = 581,516 (13.78%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,066,665 number of mapped paired reads (second in pair) = 2,068,937 number of mapped paired reads (both in pair) = 4,077,730 number of mapped paired reads (singletons) = 57,872 number of mapped bases = 470,341,447 bp number of sequenced bases = 470,028,049 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,279,091 duplication rate = 63.76% >>>>>>> Insert size mean insert size = 1,135,799.0206 std insert size = 9,940,846.3228 median insert size = 154 >>>>>>> Mapping quality mean mapping quality = 52.5577 >>>>>>> ACTG content number of A's = 139,006,301 bp (29.57%) number of C's = 94,711,177 bp (20.15%) number of T's = 137,816,130 bp (29.32%) number of G's = 98,490,655 bp (20.95%) number of N's = 3,786 bp (0%) GC percentage = 41.1% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 3,815,311 number of insertions = 49,754 mapped reads with insertion percentage = 1.16% number of deletions = 132,013 mapped reads with deletion percentage = 3.11% homopolymer indels = 41.03% >>>>>>> Coverage mean coverageData = 0.1519X std coverageData = 2.9319X There is a 3.43% of reference with a coverageData >= 1X There is a 2.53% of reference with a coverageData >= 2X There is a 1.86% of reference with a coverageData >= 3X There is a 1.48% of reference with a coverageData >= 4X There is a 1.1% of reference with a coverageData >= 5X There is a 0.91% of reference with a coverageData >= 6X There is a 0.67% of reference with a coverageData >= 7X There is a 0.58% of reference with a coverageData >= 8X There is a 0.43% of reference with a coverageData >= 9X There is a 0.38% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.19% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.12% of reference with a coverageData >= 15X There is a 0.12% of reference with a coverageData >= 16X There is a 0.08% of reference with a coverageData >= 17X There is a 0.08% of reference with a coverageData >= 18X There is a 0.06% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.03% of reference with a coverageData >= 23X There is a 0.02% of reference with a coverageData >= 24X There is a 0.02% of reference with a coverageData >= 25X There is a 0.02% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 43108963 0.17295428523726727 1.379276283818265 chr2 243199373 45455906 0.1869079900958462 9.545496666527267 chr3 198022430 31702680 0.16009640928050423 1.1835671847627147 chr4 191154276 30898977 0.16164418419810814 1.4048565398138184 chr5 180915260 28841605 0.1594205209665564 1.1747341838623437 chr6 171115067 28863073 0.16867639715209884 1.2648202303931657 chr7 159138663 26774765 0.1682480202815327 1.3385786180754813 chr8 146364022 21902881 0.1496466187571697 1.400390301724534 chr9 141213431 21177700 0.14996944589498715 1.3064239971676896 chr10 135534747 23807725 0.17565772266502258 1.6044843706869936 chr11 135006516 19009121 0.14080150768426614 1.1071065036852812 chr12 133851895 20056587 0.14984163653417085 1.1714273993595028 chr13 115169878 13305997 0.11553365542333908 1.0081012587649822 chr14 107349540 14010136 0.1305095112657213 1.0563355877049272 chr15 102531392 14032300 0.13685857303097962 1.1083972057393396 chr16 90354753 14083034 0.15586378726529196 1.263090103930582 chr17 81195210 14563890 0.17936883222544778 1.2561513010164096 chr18 78077248 11864585 0.15195956957909174 1.4937994389006202 chr19 59128983 9526586 0.1611153366192684 1.2109160967640762 chr20 63025520 10459321 0.1659537438167904 1.227307013522594 chr21 48129895 6300057 0.13089696123376127 1.210891278595309 chr22 51304566 6611616 0.12886993333108013 1.1138374580641333 chrMT 16571 524277 31.63822340232937 28.338190907261577 chrX 155270560 10741794 0.06918113775077517 0.7606432164597813 chrY 59373566 2717871 0.04577577503092875 0.8203813750523199