BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237335.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 = 3,431,655 number of mapped reads = 3,042,343 (88.66%) number of supplementary alignments = 29,079 (0.85%) number of secondary alignments = 0 number of mapped bases = 178,681,849 bp number of sequenced bases = 178,572,011 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,302,943 duplication rate = 26.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.2887 >>>>>>> ACTG content number of A's = 44,502,060 bp (24.92%) number of C's = 30,370,933 bp (17.01%) number of T's = 60,402,888 bp (33.83%) number of G's = 43,279,213 bp (24.24%) number of N's = 16,917 bp (0.01%) GC percentage = 41.24% >>>>>>> Mismatches and indels general error rate = 0.0071 number of mismatches = 1,236,928 number of insertions = 12,131 mapped reads with insertion percentage = 0.39% number of deletions = 63,480 mapped reads with deletion percentage = 2.06% homopolymer indels = 40.63% >>>>>>> Coverage mean coverageData = 0.0577X std coverageData = 1.0078X There is a 1.8% of reference with a coverageData >= 1X There is a 1.04% of reference with a coverageData >= 2X There is a 0.74% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.28% of reference with a coverageData >= 6X There is a 0.21% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.11% 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 0.03% 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 0.01% 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% 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 14189716 0.056929511120455745 0.6875516742645494 chr2 243199373 15270773 0.06279116928479911 1.4787565991508138 chr3 198022430 7877944 0.039783089218731436 0.4892749302267527 chr4 191154276 4566948 0.0238914247463656 0.3852705089544034 chr5 180915260 5420909 0.02996380183739061 0.4269710827340107 chr6 171115067 25883833 0.15126565681092244 2.1429231366477723 chr7 159138663 13056650 0.08204574396857915 1.4512162475134862 chr8 146364022 14717721 0.10055559282184798 1.1771371817962326 chr9 141213431 6564675 0.04648761065794089 0.6488832965767439 chr10 135534747 5401048 0.03984991391174397 0.6031096445273759 chr11 135006516 6054767 0.0448479612643289 0.806963423994704 chr12 133851895 4056571 0.030306414414229998 0.4427097742381444 chr13 115169878 3410481 0.029612612770155058 0.5192136880212689 chr14 107349540 4591818 0.04277445436654875 0.519177848254012 chr15 102531392 5240658 0.05111271677653611 0.6030322221158563 chr16 90354753 4032284 0.04462724833081 0.6403395622239907 chr17 81195210 6353412 0.07824860604461766 0.9141367826484705 chr18 78077248 1986931 0.025448271434976806 2.3252674155883546 chr19 59128983 3786174 0.06403245596157134 0.718174559202536 chr20 63025520 5801456 0.09204931589616397 0.7700434980775795 chr21 48129895 3589651 0.07458256453707202 0.6860954500250749 chr22 51304566 1612455 0.03142907397364983 0.42626915421178174 chrMT 16571 12116 0.7311568402631102 2.3351475397199155 chrX 155270560 14437556 0.092983215878142 0.8209478546389695 chrY 59373566 765302 0.012889608146494013 0.34168441341425076