BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524431.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 = 2,213,690 number of mapped reads = 2,024,089 (91.44%) number of supplementary alignments = 8,943 (0.4%) number of secondary alignments = 0 number of mapped bases = 118,446,168 bp number of sequenced bases = 118,412,095 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 117,882 duplication rate = 4.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7651 >>>>>>> ACTG content number of A's = 28,612,814 bp (24.16%) number of C's = 24,003,705 bp (20.27%) number of T's = 36,344,341 bp (30.69%) number of G's = 29,438,753 bp (24.86%) number of N's = 12,482 bp (0.01%) GC percentage = 45.13% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 610,432 number of insertions = 7,411 mapped reads with insertion percentage = 0.36% number of deletions = 21,115 mapped reads with deletion percentage = 1.04% homopolymer indels = 41.95% >>>>>>> Coverage mean coverageData = 0.0383X std coverageData = 0.3865X There is a 3.28% of reference with a coverageData >= 1X There is a 0.38% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 9630761 0.03863886461490501 0.7988853112180282 chr2 243199373 9933044 0.04084321385154229 0.5176373877611228 chr3 198022430 7718092 0.03897584733204213 0.22460976625159773 chr4 191154276 7386030 0.03863910425943074 0.3068946449660852 chr5 180915260 6864359 0.03794239910994794 0.22226330334392497 chr6 171115067 6589102 0.03850684872770438 0.24688709526768599 chr7 159138663 6549597 0.041156541575317875 0.4755478084302752 chr8 146364022 5863552 0.040061429850568056 0.2957766022105605 chr9 141213431 4971629 0.03520648825535582 0.27651390052996516 chr10 135534747 5806118 0.04283859400276152 0.42224243764145974 chr11 135006516 5446271 0.040340801032151666 0.30876658296313364 chr12 133851895 5378897 0.04018543779301743 0.23513505120335523 chr13 115169878 3559787 0.030909010774501297 0.20010303275541103 chr14 107349540 3547057 0.03304212575107448 0.21174605742670527 chr15 102531392 3593882 0.03505152841385397 0.21294108470486564 chr16 90354753 3680041 0.04072880371882595 0.25336711993144434 chr17 81195210 3399935 0.0418735908189658 0.2560567529852916 chr18 78077248 3045574 0.03900718939274089 0.5294294457527126 chr19 59128983 2734731 0.04625026275185555 0.511080047801802 chr20 63025520 2725315 0.0432414520340332 0.2593779708546476 chr21 48129895 1580919 0.03284692393365911 0.2844343149825417 chr22 51304566 1561806 0.03044185190066709 0.20083894043637265 chrMT 16571 14288 0.8622291955826443 1.143739633095619 chrX 155270560 6410204 0.041284091459449876 0.2560777226340483 chrY 59373566 455177 0.0076663241012001875 0.2552758485023092