BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6230346.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 = 1,011,721 number of mapped reads = 942,966 (93.2%) number of supplementary alignments = 8,088 (0.8%) number of secondary alignments = 0 number of mapped bases = 66,761,111 bp number of sequenced bases = 66,724,427 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 28,186 duplication rate = 2.22% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.9482 >>>>>>> ACTG content number of A's = 20,237,662 bp (30.33%) number of C's = 13,085,813 bp (19.61%) number of T's = 20,023,075 bp (30.01%) number of G's = 13,341,663 bp (20%) number of N's = 36,214 bp (0.05%) GC percentage = 39.61% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 623,713 number of insertions = 6,036 mapped reads with insertion percentage = 0.64% number of deletions = 21,921 mapped reads with deletion percentage = 2.29% homopolymer indels = 45.75% >>>>>>> Coverage mean coverageData = 0.0216X std coverageData = 0.2536X There is a 1.74% of reference with a coverageData >= 1X There is a 0.29% of reference with a coverageData >= 2X There is a 0.06% 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% 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 4701084 0.018860871764889205 0.3660365871319698 chr2 243199373 4462619 0.0183496320115924 0.23822149366634998 chr3 198022430 3736514 0.01886914527813844 0.16508084428336725 chr4 191154276 5305222 0.027753614049418385 0.20530278416179598 chr5 180915260 4540125 0.02509531257893889 0.18970259348487492 chr6 171115067 4621448 0.02700783794801658 0.2525351868893013 chr7 159138663 2948430 0.018527427241235527 0.38717703886281485 chr8 146364022 3781924 0.02583916421755614 0.2530746564037098 chr9 141213431 2903630 0.020561995976147624 0.2452379682646042 chr10 135534747 2716433 0.020042336449707616 0.2465651027527057 chr11 135006516 4363703 0.032322165842721254 0.3353838426435401 chr12 133851895 3781627 0.028252323211412137 0.20323774862257965 chr13 115169878 2173209 0.018869595398894146 0.16405724336343616 chr14 107349540 1965638 0.01831063272371731 0.16986652675650626 chr15 102531392 1890507 0.01843832374771621 0.16094550896887289 chr16 90354753 2119602 0.023458666308345727 0.21865968539241493 chr17 81195210 1216394 0.014981105412499087 0.17188503261677565 chr18 78077248 2391640 0.030631714888311637 0.5056678734622898 chr19 59128983 1057207 0.01787967501487384 0.27348134949405956 chr20 63025520 1463930 0.023227575115603964 0.18660755261421924 chr21 48129895 717597 0.014909589975211872 0.16110139237446364 chr22 51304566 699758 0.013639292845786865 0.13613094722255353 chrMT 16571 2416 0.1457968740570877 0.4101075236082027 chrX 155270560 3038066 0.019566271932039143 0.18644256530444564 chrY 59373566 162388 0.002735021844569686 0.09234117689220372