BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716211.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 = 6,357,344 number of mapped reads = 5,796,255 (91.17%) number of supplementary alignments = 137,601 (2.16%) number of secondary alignments = 0 number of mapped bases = 423,646,016 bp number of sequenced bases = 423,509,661 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 416,015 duplication rate = 5.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7564 >>>>>>> ACTG content number of A's = 111,552,306 bp (26.34%) number of C's = 89,838,100 bp (21.21%) number of T's = 123,260,966 bp (29.1%) number of G's = 98,808,844 bp (23.33%) number of N's = 49,445 bp (0.01%) GC percentage = 44.54% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 3,119,840 number of insertions = 31,415 mapped reads with insertion percentage = 0.54% number of deletions = 79,614 mapped reads with deletion percentage = 1.36% homopolymer indels = 40.46% >>>>>>> Coverage mean coverageData = 0.1369X std coverageData = 0.9087X There is a 9.4% of reference with a coverageData >= 1X There is a 2.54% of reference with a coverageData >= 2X There is a 0.86% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 33839066 0.13576321641341066 1.090498082464983 chr2 243199373 36033620 0.14816493790878318 1.4566967505920148 chr3 198022430 27996117 0.14137851454504421 0.5171123445322814 chr4 191154276 26578264 0.1390409074605268 0.5771832002407222 chr5 180915260 25352640 0.14013544241652143 0.526292594687189 chr6 171115067 24495296 0.14315101778851538 0.6542540298378029 chr7 159138663 23184503 0.14568743109271945 1.2040855998634883 chr8 146364022 21921699 0.1497751886047515 1.2377126210781724 chr9 141213431 17920031 0.1269003300401362 0.9855758363786459 chr10 135534747 20374340 0.15032558403639473 0.8555284519125727 chr11 135006516 19383970 0.14357803292990687 1.0127898493307244 chr12 133851895 19725630 0.1473690753500352 0.5481992899727529 chr13 115169878 13097893 0.11372672462151953 0.4656613593767222 chr14 107349540 12876453 0.11994884188604814 0.6335616310605374 chr15 102531392 12316621 0.12012536609275723 0.49032963988465406 chr16 90354753 12730605 0.14089579770086916 0.6197769469631018 chr17 81195210 11800979 0.14534082737146686 0.6217886962946829 chr18 78077248 11206312 0.14352852190691967 1.844848183652106 chr19 59128983 8804829 0.14890885236433035 0.9822042428993818 chr20 63025520 9111049 0.14456126661073165 0.5687104327180698 chr21 48129895 5639254 0.11716738629909747 0.5392945981778218 chr22 51304566 5126825 0.09992921487728793 0.4488677458221562 chrMT 16571 75376 4.548669362138676 5.009134043341593 chrX 155270560 23044866 0.14841748493726048 0.7871601753568256 chrY 59373566 1009778 0.0170071981191091 0.3978275857288411