BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524336.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 = 1,354,017 number of mapped reads = 1,236,829 (91.35%) number of supplementary alignments = 5,522 (0.41%) number of secondary alignments = 0 number of mapped bases = 71,669,539 bp number of sequenced bases = 71,651,320 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 35,064 duplication rate = 2.05% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9654 >>>>>>> ACTG content number of A's = 18,438,906 bp (25.73%) number of C's = 13,593,603 bp (18.97%) number of T's = 21,683,784 bp (30.26%) number of G's = 17,924,626 bp (25.02%) number of N's = 10,401 bp (0.01%) GC percentage = 43.99% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 358,372 number of insertions = 5,502 mapped reads with insertion percentage = 0.44% number of deletions = 11,218 mapped reads with deletion percentage = 0.9% homopolymer indels = 41.63% >>>>>>> Coverage mean coverageData = 0.0232X std coverageData = 0.2262X There is a 2.12% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% 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 6081736 0.024400083641115584 0.39074895154260136 chr2 243199373 4639793 0.01907814540294888 0.30970816511059335 chr3 198022430 4980807 0.025152741535390714 0.16937261709606605 chr4 191154276 3698415 0.019347801563172985 0.16198097942827153 chr5 180915260 4207018 0.02325408039100737 0.1629737269617547 chr6 171115067 4498994 0.026292214232660177 0.18160176124802457 chr7 159138663 3232166 0.0203103754868168 0.25057970621744713 chr8 146364022 7404003 0.05058622261692153 0.2869602396362535 chr9 141213431 2974630 0.02106478101222539 0.17978953691333013 chr10 135534747 3634139 0.026813338132397887 0.22121052856954795 chr11 135006516 3458383 0.025616415432866958 0.1993742119461201 chr12 133851895 2814452 0.021026613033756452 0.15649420582805285 chr13 115169878 1767232 0.01534456778707363 0.13187879610787437 chr14 107349540 1529472 0.01424758783316631 0.13180737076992655 chr15 102531392 2220195 0.021653807255440364 0.1576904578519436 chr16 90354753 2275648 0.025185703291115188 0.17606325488027055 chr17 81195210 2253865 0.02775859561173621 0.1918874950639248 chr18 78077248 1653883 0.02118264977782004 0.287032479089774 chr19 59128983 1336910 0.022610062479850195 0.260988658004879 chr20 63025520 1652114 0.026213413233242663 0.17456927420147814 chr21 48129895 1017777 0.021146462089726148 0.16238198272477086 chr22 51304566 539280 0.01051134513056791 0.1090945611082401 chrMT 16571 166173 10.02794037776839 5.965871830115036 chrX 155270560 3437856 0.022141067823803817 0.17120515572708767 chrY 59373566 194598 0.003277519157262678 0.09491872073486086