BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524655.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 = 1,753,014 number of mapped reads = 1,594,194 (90.94%) number of supplementary alignments = 5,356 (0.31%) number of secondary alignments = 0 number of mapped bases = 91,504,285 bp number of sequenced bases = 91,480,648 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 43,681 duplication rate = 1.81% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5767 >>>>>>> ACTG content number of A's = 23,841,589 bp (26.06%) number of C's = 16,378,695 bp (17.9%) number of T's = 28,599,013 bp (31.26%) number of G's = 22,658,685 bp (24.77%) number of N's = 2,666 bp (0%) GC percentage = 42.67% >>>>>>> Mismatches and indels general error rate = 0.0049 number of mismatches = 439,817 number of insertions = 5,946 mapped reads with insertion percentage = 0.37% number of deletions = 14,504 mapped reads with deletion percentage = 0.91% homopolymer indels = 42.59% >>>>>>> Coverage mean coverageData = 0.0296X std coverageData = 0.2747X There is a 2.67% of reference with a coverageData >= 1X There is a 0.2% 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 6556557 0.026305077891862105 0.45265235836214074 chr2 243199373 7689467 0.0316179556926736 0.32049171075089405 chr3 198022430 5517271 0.027861848781473898 0.17827097554333884 chr4 191154276 5644068 0.029526245073377276 0.20263759160038064 chr5 180915260 5098953 0.028184206241087677 0.18349869480563025 chr6 171115067 4848450 0.0283344423434086 0.1989015131902384 chr7 159138663 5786202 0.03635949863421939 0.37577545839197796 chr8 146364022 3982135 0.02720706185567926 0.259405351556003 chr9 141213431 4211185 0.029821419748663994 0.2890235406324374 chr10 135534747 3401902 0.025099851331850716 0.26066061832143467 chr11 135006516 3573873 0.026471855625101827 0.23729632832538866 chr12 133851895 6719258 0.0501991996452497 0.27122932017332374 chr13 115169878 3392249 0.029454307488282656 0.1830563802338979 chr14 107349540 3200798 0.0298165972578923 0.20648090132392666 chr15 102531392 2322386 0.02265048737463742 0.1635334539935317 chr16 90354753 2537318 0.02808173245739491 0.19853415622087933 chr17 81195210 3123518 0.03846923974948768 0.2202830090854548 chr18 78077248 2868637 0.03674101064627688 0.4955863039242502 chr19 59128983 1447415 0.024478942923811153 0.3459047066443833 chr20 63025520 2592531 0.04113462292734753 0.22526758720930382 chr21 48129895 1076641 0.022369485742696926 0.18053861538984614 chr22 51304566 816555 0.01591583485961074 0.13423556388159044 chrMT 16571 3939 0.2377044233902601 0.509528878532719 chrX 155270560 4843524 0.03119409114000748 0.2316279375287603 chrY 59373566 249453 0.004201415155020333 0.10182825638035171