BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524339.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 = 2,020,972 number of mapped reads = 1,831,431 (90.62%) number of supplementary alignments = 8,789 (0.43%) number of secondary alignments = 0 number of mapped bases = 105,260,442 bp number of sequenced bases = 105,231,865 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 64,564 duplication rate = 2.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2068 >>>>>>> ACTG content number of A's = 24,577,994 bp (23.36%) number of C's = 20,598,764 bp (19.57%) number of T's = 34,734,302 bp (33.01%) number of G's = 25,306,587 bp (24.05%) number of N's = 14,218 bp (0.01%) GC percentage = 43.62% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 546,890 number of insertions = 7,086 mapped reads with insertion percentage = 0.38% number of deletions = 18,150 mapped reads with deletion percentage = 0.98% homopolymer indels = 42.99% >>>>>>> Coverage mean coverageData = 0.034X std coverageData = 0.3229X There is a 3.04% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.04% 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 8869357 0.03558409188477007 0.6120388509214193 chr2 243199373 6774528 0.027855861289576598 0.4503193191233886 chr3 198022430 7396929 0.03735399570644598 0.21362030561151496 chr4 191154276 5518865 0.028871261033156275 0.20690932769648465 chr5 180915260 6216723 0.0343626236946513 0.20325980113810133 chr6 171115067 6784684 0.039649833991532726 0.24005459316235728 chr7 159138663 4833981 0.030375905571105623 0.4041266242686322 chr8 146364022 11025037 0.07532614128354576 0.38590679814939904 chr9 141213431 4344716 0.03076701677193864 0.24733201361134688 chr10 135534747 5331656 0.03933792712211283 0.3056133463429409 chr11 135006516 5049422 0.03740132068884734 0.2698843482210897 chr12 133851895 4138193 0.030916207798178726 0.19757824506937643 chr13 115169878 2690735 0.02336318355742289 0.16785987016455645 chr14 107349540 2229920 0.020772515653071266 0.1698752596861837 chr15 102531392 3210904 0.03131630164545118 0.1978569788051914 chr16 90354753 3292775 0.036442742530655804 0.22485083425162602 chr17 81195210 3166373 0.03899704182057045 0.24258734827205009 chr18 78077248 2476789 0.031722288674928704 0.45638368075247887 chr19 59128983 1869699 0.03162068591641429 0.4119955473359767 chr20 63025520 2365875 0.03753836541134448 0.21486943937296135 chr21 48129895 1512757 0.03143071473561287 0.206340611994728 chr22 51304566 750234 0.01462314289921096 0.1321733814985069 chrMT 16571 6742 0.40685534970732 0.6584737406653449 chrX 155270560 5098270 0.03283474987145019 0.22865409239970713 chrY 59373566 305278 0.005141648389453313 0.13652354745742457