BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716706.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 = 3,713,575 number of mapped reads = 3,152,632 (84.89%) number of supplementary alignments = 9,763 (0.26%) number of secondary alignments = 0 number of mapped bases = 180,004,805 bp number of sequenced bases = 179,946,925 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 168,238 duplication rate = 3.98% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0648 >>>>>>> ACTG content number of A's = 44,344,494 bp (24.64%) number of C's = 33,887,979 bp (18.83%) number of T's = 57,816,552 bp (32.13%) number of G's = 43,895,056 bp (24.39%) number of N's = 2,844 bp (0%) GC percentage = 43.23% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 923,123 number of insertions = 13,026 mapped reads with insertion percentage = 0.41% number of deletions = 36,168 mapped reads with deletion percentage = 1.14% homopolymer indels = 42.62% >>>>>>> Coverage mean coverageData = 0.0581X std coverageData = 0.4343X There is a 4.82% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.14% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 14348801 0.057567764294557164 0.6177185053289963 chr2 243199373 15237745 0.06265536301362093 0.6729153230490987 chr3 198022430 11989696 0.060547161248349496 0.2935073342359562 chr4 191154276 11661135 0.061003788374579704 0.35466437045877447 chr5 180915260 10769348 0.05952702939486697 0.287325437333975 chr6 171115067 10363641 0.06056533291717672 0.35007890842631906 chr7 159138663 9927620 0.06238345737515716 0.632304212240569 chr8 146364022 9144169 0.06247552421045112 0.41209825981434445 chr9 141213431 7430095 0.05261606454417215 0.34972526505413754 chr10 135534747 8722026 0.0643526932617508 0.5172839612563755 chr11 135006516 8018428 0.059392896265836534 0.38574046962756836 chr12 133851895 8204899 0.06129834022895231 0.2960473148859914 chr13 115169878 5617743 0.048777884439540696 0.2629940546201715 chr14 107349540 5524299 0.05146085395428802 0.28541264052231863 chr15 102531392 5196028 0.0506774354531342 0.27146126948679317 chr16 90354753 5367639 0.05940627163243974 0.33454367097385984 chr17 81195210 5061295 0.06233489635657079 0.33393233423043595 chr18 78077248 4726553 0.060536880090855665 0.6381701785521001 chr19 59128983 3818175 0.06457366263174187 0.5380543497649418 chr20 63025520 3795705 0.06022488985414162 0.3049568968022729 chr21 48129895 2346101 0.0487451925669067 0.3062964285344014 chr22 51304566 2163128 0.04216248510902519 0.24318688284546802 chrMT 16571 24041 1.450787520366906 1.621701276174556 chrX 155270560 10002582 0.06442033827919472 0.3448725394082584 chrY 59373566 543913 0.009160861249263687 0.23169996569010823