BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716215.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 = 1,736,185 number of mapped reads = 1,551,611 (89.37%) number of supplementary alignments = 7,274 (0.42%) number of secondary alignments = 0 number of mapped bases = 88,885,367 bp number of sequenced bases = 88,861,224 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 38,675 duplication rate = 1.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9528 >>>>>>> ACTG content number of A's = 21,969,603 bp (24.72%) number of C's = 17,246,129 bp (19.41%) number of T's = 26,335,862 bp (29.64%) number of G's = 23,307,807 bp (26.23%) number of N's = 1,823 bp (0%) GC percentage = 45.64% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 452,594 number of insertions = 4,856 mapped reads with insertion percentage = 0.31% number of deletions = 14,068 mapped reads with deletion percentage = 0.9% homopolymer indels = 43.82% >>>>>>> Coverage mean coverageData = 0.0287X std coverageData = 0.2286X There is a 2.6% of reference with a coverageData >= 1X There is a 0.2% of reference with a coverageData >= 2X There is a 0.03% 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 9998890 0.04011580777566047 0.331927281035051 chr2 243199373 7497845 0.030830034253418903 0.2598877168704924 chr3 198022430 5891549 0.029751927597292893 0.18741035636439798 chr4 191154276 5614743 0.029372834955572743 0.20063967870139537 chr5 180915260 4438577 0.024534011116585742 0.171680842300686 chr6 171115067 4708026 0.02751380157540423 0.19010930859143876 chr7 159138663 3767188 0.023672361756614732 0.20370068141612235 chr8 146364022 5604202 0.038289477997536854 0.23927521443242333 chr9 141213431 3247990 0.0230005742159186 0.22777105181049614 chr10 135534747 4153418 0.030644672985592397 0.2604320272397495 chr11 135006516 2759765 0.02044171705016075 0.19560157001433848 chr12 133851895 3984255 0.029766145634322175 0.18925067096114542 chr13 115169878 2728056 0.02368723530296698 0.16592963272183117 chr14 107349540 3098616 0.028864734772035352 0.19505004301940976 chr15 102531392 2513381 0.024513282722232035 0.16880607359905042 chr16 90354753 2768446 0.030639738454046796 0.20672529740383094 chr17 81195210 1950897 0.02402724249373824 0.1718657180801205 chr18 78077248 2175529 0.02786380226926031 0.44493990714430526 chr19 59128983 1780929 0.030119391703388506 0.26304302793215034 chr20 63025520 2846938 0.04517119414484799 0.23587414762083372 chr21 48129895 1181433 0.024546760386657814 0.1898854667552455 chr22 51304566 1029671 0.020069773127015633 0.1532852057586381 chrMT 16571 1047 0.06318266851728924 0.24747201077588168 chrX 155270560 4884857 0.03146029099141524 0.21261981104332167 chrY 59373566 259119 0.00436421487636434 0.10488087403165619