BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525019.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 = 1,772,200 number of mapped reads = 1,592,371 (89.85%) number of supplementary alignments = 6,143 (0.35%) number of secondary alignments = 0 number of mapped bases = 90,543,767 bp number of sequenced bases = 90,515,122 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 46,848 duplication rate = 2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.5491 >>>>>>> ACTG content number of A's = 21,615,831 bp (23.88%) number of C's = 18,397,848 bp (20.33%) number of T's = 28,934,525 bp (31.97%) number of G's = 21,566,072 bp (23.83%) number of N's = 846 bp (0%) GC percentage = 44.15% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 463,954 number of insertions = 5,646 mapped reads with insertion percentage = 0.35% number of deletions = 17,433 mapped reads with deletion percentage = 1.09% homopolymer indels = 43.32% >>>>>>> Coverage mean coverageData = 0.0292X std coverageData = 0.2597X There is a 2.66% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 9551699 0.03832166580640134 0.4391064882976302 chr2 243199373 8568030 0.03523047734173229 0.32219704869879245 chr3 198022430 4932058 0.024906562352557737 0.17223069765495908 chr4 191154276 5636657 0.029487475341644986 0.19973140757134367 chr5 180915260 3931861 0.021733163913314996 0.1627830689478836 chr6 171115067 6039509 0.03529501583866954 0.2795456577432097 chr7 159138663 5730262 0.03600798129113351 0.3731598858400638 chr8 146364022 5265571 0.03597585614311692 0.2482564460176659 chr9 141213431 2489311 0.017628004520334896 0.1993881708296953 chr10 135534747 4538976 0.03348938999384416 0.2669203618308632 chr11 135006516 3720014 0.02755432930363154 0.23392396555245046 chr12 133851895 4799861 0.03585949231424777 0.20684475308859618 chr13 115169878 2439767 0.02118407210607621 0.15808217429246565 chr14 107349540 2024256 0.018856680708645795 0.15538914237991866 chr15 102531392 2517368 0.024552168373955168 0.18051304009547645 chr16 90354753 2929901 0.032426639470753686 0.20698240089646172 chr17 81195210 2427785 0.029900593889713445 0.2537029633413908 chr18 78077248 1775093 0.022735086666989084 0.30829629685162285 chr19 59128983 2359174 0.039898775191178244 0.30430294840482364 chr20 63025520 2237114 0.0354953675907791 0.2080921622982049 chr21 48129895 1286977 0.026739659415421536 0.18331673030023782 chr22 51304566 1293975 0.02522143935492993 0.17111951837417752 chrMT 16571 13961 0.8424959266187919 1.0612637812952652 chrX 155270560 3776698 0.024323335988483585 0.2099428552287013 chrY 59373566 257889 0.004343498586559548 0.0984737465011404