BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237830.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,073,837 number of mapped reads = 1,760,476 (84.89%) number of supplementary alignments = 20,446 (0.99%) number of secondary alignments = 0 number of mapped bases = 115,647,401 bp number of sequenced bases = 115,600,633 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 452,513 duplication rate = 14.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8408 >>>>>>> ACTG content number of A's = 31,770,345 bp (27.48%) number of C's = 21,475,820 bp (18.58%) number of T's = 36,421,581 bp (31.51%) number of G's = 25,735,894 bp (22.26%) number of N's = 196,993 bp (0.17%) GC percentage = 40.84% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 959,685 number of insertions = 7,799 mapped reads with insertion percentage = 0.44% number of deletions = 26,973 mapped reads with deletion percentage = 1.52% homopolymer indels = 46.14% >>>>>>> Coverage mean coverageData = 0.0374X std coverageData = 0.5875X There is a 1.01% of reference with a coverageData >= 1X There is a 0.6% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.36% of reference with a coverageData >= 4X There is a 0.28% of reference with a coverageData >= 5X There is a 0.21% of reference with a coverageData >= 6X There is a 0.17% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.1% of reference with a coverageData >= 9X There is a 0.08% of reference with a coverageData >= 10X There is a 0.06% of reference with a coverageData >= 11X There is a 0.05% of reference with a coverageData >= 12X There is a 0.04% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% 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 8497628 0.034092705430009744 0.7333741271567491 chr2 243199373 10858827 0.044649897185384604 0.7200405358482702 chr3 198022430 7169257 0.036204267365065664 0.5384128197614029 chr4 191154276 7768939 0.04064224542902718 0.5652331469224678 chr5 180915260 7139551 0.03946350904837989 0.5646783866899214 chr6 171115067 7394576 0.04321405548700162 0.6056848820966371 chr7 159138663 6360932 0.0399710031496243 0.6013520230317804 chr8 146364022 7154022 0.04887828239647582 0.6553553479620084 chr9 141213431 4530663 0.032083796618467546 0.522402194171308 chr10 135534747 4750820 0.03505241353348304 0.5537377009994802 chr11 135006516 5143402 0.03809743523786659 0.5559088514835654 chr12 133851895 4798755 0.035851229450281595 0.5352171306313976 chr13 115169878 2845975 0.024711105450680428 0.44114088747608077 chr14 107349540 3946296 0.036761182209071416 0.549152798770045 chr15 102531392 4229367 0.04124948386539022 0.5805407673768678 chr16 90354753 2800729 0.030997030117496972 0.48289425337807246 chr17 81195210 2677877 0.03298072632609732 0.4980530447862965 chr18 78077248 3407309 0.043640229225292364 0.6749742123732269 chr19 59128983 3350912 0.05667122669774313 0.8154992036401745 chr20 63025520 2292938 0.03638110403531776 0.5487325631429042 chr21 48129895 1313886 0.02729875059980912 0.45371520401214316 chr22 51304566 899319 0.017529024609622464 0.34554953101040337 chrMT 16571 46551 2.8091847202944904 4.910894057147562 chrX 155270560 6002687 0.03865953082155432 0.5476266241922467 chrY 59373566 266183 0.00448319038138959 0.13967651568450873