BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238294.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 = 840,264 number of mapped reads = 322,163 (38.34%) number of supplementary alignments = 3,968 (0.47%) number of secondary alignments = 0 number of mapped bases = 20,614,772 bp number of sequenced bases = 20,602,887 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,453 duplication rate = 7.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.0546 >>>>>>> ACTG content number of A's = 5,831,223 bp (28.3%) number of C's = 3,809,280 bp (18.49%) number of T's = 6,508,721 bp (31.59%) number of G's = 4,448,846 bp (21.59%) number of N's = 4,817 bp (0.02%) GC percentage = 40.08% >>>>>>> Mismatches and indels general error rate = 0.0097 number of mismatches = 197,008 number of insertions = 1,876 mapped reads with insertion percentage = 0.58% number of deletions = 7,229 mapped reads with deletion percentage = 2.21% homopolymer indels = 45.67% >>>>>>> Coverage mean coverageData = 0.0067X std coverageData = 0.1329X There is a 0.43% of reference with a coverageData >= 1X There is a 0.13% 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 0.01% 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 1624227 0.006516441136569927 0.15713867071248588 chr2 243199373 1796834 0.00738831674537253 0.14206965997294366 chr3 198022430 1260288 0.006364369935264404 0.12073926700341937 chr4 191154276 1199390 0.006274460739763938 0.1297245320685818 chr5 180915260 1250753 0.006913474297303611 0.12727723560418364 chr6 171115067 1161912 0.0067902378228329825 0.12665341014889844 chr7 159138663 1104734 0.006941958535871324 0.13794888580585077 chr8 146364022 1137727 0.007773269581236296 0.16101091004140503 chr9 141213431 844478 0.005980153545026464 0.12094921902587089 chr10 135534747 956005 0.007053578666435995 0.13197733408580445 chr11 135006516 1062041 0.007866590676260396 0.1408414990761099 chr12 133851895 971973 0.007261555766543313 0.13012905124990112 chr13 115169878 725749 0.006301552216630811 0.12161882340071745 chr14 107349540 670200 0.006243156700997508 0.13218132162579627 chr15 102531392 594242 0.0057957079135334474 0.13414232516756106 chr16 90354753 527703 0.005840345775722501 0.1128256230845182 chr17 81195210 494307 0.006087883755704308 0.11868682115561444 chr18 78077248 634097 0.008121405611017438 0.15748867920803625 chr19 59128983 337524 0.005708266621125549 0.12830627179361767 chr20 63025520 425525 0.006751630133317425 0.1218456016345709 chr21 48129895 322611 0.006702923411738173 0.12092800043954628 chr22 51304566 212520 0.00414232136765371 0.09339396094252692 chrMT 16571 5374 0.3243014905557902 0.9114596064491095 chrX 155270560 1230568 0.00792531436738555 0.13351574850633288 chrY 59373566 63990 0.0010777523452103247 0.05135599957108384