BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238273.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 = 2,636,589 number of mapped reads = 2,433,769 (92.31%) number of supplementary alignments = 22,122 (0.84%) number of secondary alignments = 0 number of mapped bases = 163,248,600 bp number of sequenced bases = 163,164,898 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 102,031 duplication rate = 3.11% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2116 >>>>>>> ACTG content number of A's = 46,583,506 bp (28.55%) number of C's = 30,769,583 bp (18.86%) number of T's = 50,587,082 bp (31%) number of G's = 35,186,132 bp (21.56%) number of N's = 38,595 bp (0.02%) GC percentage = 40.42% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,428,232 number of insertions = 13,642 mapped reads with insertion percentage = 0.56% number of deletions = 50,611 mapped reads with deletion percentage = 2.05% homopolymer indels = 46.76% >>>>>>> Coverage mean coverageData = 0.0527X std coverageData = 0.4606X There is a 4.31% of reference with a coverageData >= 1X There is a 0.69% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 12747254 0.05114231591021793 0.7343753340934797 chr2 243199373 14305767 0.05882320675226412 0.5161554533201567 chr3 198022430 10946697 0.05528008620033599 0.27447921816690013 chr4 191154276 10646755 0.05569718461333295 0.30445591902245045 chr5 180915260 10611235 0.05865306774011214 0.28732687376924965 chr6 171115067 9779567 0.05715199234910155 0.35682938073995557 chr7 159138663 9383888 0.05896673896273717 0.7215586978908234 chr8 146364022 7790114 0.05322424113215473 0.7551348122137332 chr9 141213431 6717360 0.04756884633728643 0.4266948203944109 chr10 135534747 7588712 0.05599089656322596 0.4198334145282551 chr11 135006516 7297263 0.05405119112917483 0.37942811141566557 chr12 133851895 6994800 0.052257758472526665 0.27664231009218376 chr13 115169878 5539892 0.04810191776012822 0.2574285612067822 chr14 107349540 5212811 0.048559229969685945 0.3110853360736988 chr15 102531392 4872128 0.04751840294921579 0.2605354022951373 chr16 90354753 3981728 0.0440677204883732 0.2849957783064568 chr17 81195210 4138985 0.05097572874064862 0.31620890710995375 chr18 78077248 4743682 0.06075626538476356 0.8444698344954817 chr19 59128983 3014173 0.050976236137868294 0.51292745279498 chr20 63025520 2934414 0.04655913985318963 0.2631993767957668 chr21 48129895 2220129 0.04612785878714259 0.2875997610651959 chr22 51304566 1721406 0.033552686129339836 0.21279843435788384 chrMT 16571 6770 0.40854504857884255 0.756121483452309 chrX 155270560 9616072 0.06193107051330272 0.3366596357101815 chrY 59373566 436998 0.0073601440748901625 0.20019432316685662