BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524344.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,515,123 number of mapped reads = 1,375,277 (90.77%) number of supplementary alignments = 5,426 (0.36%) number of secondary alignments = 0 number of mapped bases = 79,263,039 bp number of sequenced bases = 79,236,232 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 55,689 duplication rate = 3.06% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3981 >>>>>>> ACTG content number of A's = 19,638,008 bp (24.78%) number of C's = 14,960,494 bp (18.88%) number of T's = 26,710,018 bp (33.71%) number of G's = 17,926,106 bp (22.62%) number of N's = 1,606 bp (0%) GC percentage = 41.5% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 411,540 number of insertions = 5,484 mapped reads with insertion percentage = 0.4% number of deletions = 16,706 mapped reads with deletion percentage = 1.2% homopolymer indels = 43.22% >>>>>>> Coverage mean coverageData = 0.0256X std coverageData = 0.2564X There is a 2.32% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 6335253 0.02541720046506925 0.41797959817274355 chr2 243199373 6704994 0.027569947723508317 0.3807843071538537 chr3 198022430 5236179 0.02644235302031189 0.17653679437447783 chr4 191154276 5158394 0.026985501490952784 0.1899664424355304 chr5 180915260 4796402 0.026511870806254816 0.17712249492428953 chr6 171115067 4675702 0.0273248994490941 0.19756879704622507 chr7 159138663 4432276 0.027851660410141813 0.3491401933740011 chr8 146364022 3987846 0.027246081007530662 0.28431422583128135 chr9 141213431 3337528 0.02363463571676833 0.21332481763787972 chr10 135534747 3779845 0.027888383485896794 0.2455533818311937 chr11 135006516 3559864 0.026368090263139594 0.21434491594232014 chr12 133851895 3588288 0.02680789838649651 0.1794150272523938 chr13 115169878 2581327 0.02241321294097403 0.16293752364800157 chr14 107349540 2398334 0.022341353302492026 0.16758391351196059 chr15 102531392 2249905 0.0219435721695849 0.1626938214260246 chr16 90354753 2280549 0.025239945041961434 0.18702514161802558 chr17 81195210 2086935 0.025702686155993686 0.18033292628555725 chr18 78077248 2095623 0.026840379927325308 0.3692077647830577 chr19 59128983 1602723 0.027105539765498756 0.3198576456420453 chr20 63025520 1629156 0.025849148091122452 0.17725936921904575 chr21 48129895 1050648 0.02182942638873407 0.1725998282773087 chr22 51304566 923307 0.017996585333165085 0.14521964095153617 chrMT 16571 4660 0.28121416933196547 0.5847178768680839 chrX 155270560 4521749 0.029121740785890127 0.20051229017525465 chrY 59373566 245552 0.004135712515566271 0.11992435844820051