BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9717087.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 = 1,628,354 number of mapped reads = 1,458,571 (89.57%) number of supplementary alignments = 23,602 (1.45%) number of secondary alignments = 0 number of mapped bases = 114,273,931 bp number of sequenced bases = 114,225,985 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 65,317 duplication rate = 2.68% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.2565 >>>>>>> ACTG content number of A's = 28,891,455 bp (25.29%) number of C's = 21,862,528 bp (19.14%) number of T's = 35,854,396 bp (31.39%) number of G's = 27,610,767 bp (24.17%) number of N's = 6,839 bp (0.01%) GC percentage = 43.31% >>>>>>> Mismatches and indels general error rate = 0.0088 number of mismatches = 980,545 number of insertions = 11,038 mapped reads with insertion percentage = 0.75% number of deletions = 27,662 mapped reads with deletion percentage = 1.87% homopolymer indels = 43.61% >>>>>>> Coverage mean coverageData = 0.0369X std coverageData = 0.4544X There is a 3.18% of reference with a coverageData >= 1X There is a 0.33% of reference with a coverageData >= 2X There is a 0.05% 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 9397270 0.037702092625879556 0.7194598306096955 chr2 243199373 10075643 0.04142955993558421 0.7106204189305306 chr3 198022430 7701192 0.03889050346468327 0.22659524731678016 chr4 191154276 7420605 0.03881997910420795 0.2415962906390218 chr5 180915260 7009586 0.03874513404784096 0.2265917241263496 chr6 171115067 6715863 0.03924764264037602 0.278589887382091 chr7 159138663 6552096 0.041172244861702775 0.5907722679319591 chr8 146364022 5903661 0.040335465774505704 0.6095449450581262 chr9 141213431 4940322 0.034984788380363056 0.5055381752979199 chr10 135534747 5587187 0.041223281288893396 0.42992190423993787 chr11 135006516 5192314 0.0384597288622721 0.406143018798242 chr12 133851895 5328111 0.03980601843552532 0.23412779217627455 chr13 115169878 3679683 0.031950046869025944 0.19841670977905998 chr14 107349540 3553700 0.03310400771163062 0.28516077715167504 chr15 102531392 3347599 0.03264950309072172 0.2069214706984955 chr16 90354753 3451283 0.038197027664941985 0.25939392133358663 chr17 81195210 3303340 0.040683927044464815 0.260585111877918 chr18 78077248 3179021 0.040716355678929665 0.9758439237304528 chr19 59128983 2614351 0.04421437453101468 0.5534563775566482 chr20 63025520 2371837 0.03763296201284813 0.23820617051170945 chr21 48129895 1491052 0.030979747618398088 0.21428243034464267 chr22 51304566 1309288 0.025519911814476708 0.1787306509735398 chrMT 16571 11723 0.707440709673526 0.9808169123704874 chrX 155270560 3851509 0.024805146577689938 0.2788392837935848 chrY 59373566 285695 0.004811821476244159 0.1492834462185926