BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472822.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 2,246,015 number of mapped reads = 1,562,468 (69.57%) number of supplementary alignments = 11,878 (0.53%) number of secondary alignments = 0 number of mapped bases = 96,531,623 bp number of sequenced bases = 96,485,265 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 132,860 duplication rate = 6.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.4065 >>>>>>> ACTG content number of A's = 25,744,525 bp (26.68%) number of C's = 19,186,204 bp (19.89%) number of T's = 28,501,824 bp (29.54%) number of G's = 23,050,522 bp (23.89%) number of N's = 2,190 bp (0%) GC percentage = 43.78% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 880,502 number of insertions = 7,128 mapped reads with insertion percentage = 0.45% number of deletions = 25,871 mapped reads with deletion percentage = 1.64% homopolymer indels = 45.9% >>>>>>> Coverage mean coverageData = 0.0312X std coverageData = 0.3032X There is a 2.22% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 7775339 0.031194863101263848 0.35248676178328403 chr2 243199373 8572715 0.03524974137166053 0.3656079389447089 chr3 198022430 6731556 0.03399390664986789 0.2610500256933999 chr4 191154276 5056517 0.026452544540515537 0.24122417805311916 chr5 180915260 5506773 0.03043841077861536 0.2549356529371118 chr6 171115067 6108922 0.03570066685010269 0.29356098423651694 chr7 159138663 5563774 0.034961799320885334 0.44169671502893415 chr8 146364022 4858079 0.03319175664631572 0.2938650387884268 chr9 141213431 4233425 0.029978911850105816 0.30622832697771607 chr10 135534747 4610328 0.0340158380197515 0.2968082066085105 chr11 135006516 3997365 0.02960868199872664 0.2956631015855118 chr12 133851895 4783058 0.03573395804370196 0.2752214458483881 chr13 115169878 3322043 0.02884472101290235 0.24847145249635094 chr14 107349540 3043256 0.028349036241794794 0.27108020360708834 chr15 102531392 2830136 0.02760262925134187 0.25763460259543564 chr16 90354753 2799006 0.030977960838429828 0.26354710754097477 chr17 81195210 2461532 0.03031622185594446 0.2698699685060576 chr18 78077248 2110479 0.02703065302711489 0.4166125401655583 chr19 59128983 1925598 0.03256605986272417 0.3063559885392355 chr20 63025520 2426459 0.03849962681783506 0.289889818006058 chr21 48129895 1370356 0.028472033857543218 0.25327657143901433 chr22 51304566 1163221 0.02267285527763747 0.22504307988583186 chrMT 16571 168186 10.149417657353208 7.662444615103747 chrX 155270560 4792112 0.030862978790055243 0.27365198577453104 chrY 59373566 321388 0.005412981258359991 0.10807562888504167