BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240243.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 = 3,195,963 number of mapped reads = 2,605,499 (81.52%) number of supplementary alignments = 26,364 (0.82%) number of secondary alignments = 0 number of mapped bases = 171,985,757 bp number of sequenced bases = 171,918,272 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 473,241 duplication rate = 12.12% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4024 >>>>>>> ACTG content number of A's = 48,310,798 bp (28.1%) number of C's = 31,369,739 bp (18.25%) number of T's = 55,086,839 bp (32.04%) number of G's = 37,133,774 bp (21.6%) number of N's = 17,122 bp (0.01%) GC percentage = 39.85% >>>>>>> Mismatches and indels general error rate = 0.008 number of mismatches = 1,352,838 number of insertions = 12,244 mapped reads with insertion percentage = 0.47% number of deletions = 39,123 mapped reads with deletion percentage = 1.49% homopolymer indels = 48.01% >>>>>>> Coverage mean coverageData = 0.0556X std coverageData = 0.6528X There is a 2.19% of reference with a coverageData >= 1X There is a 1.24% of reference with a coverageData >= 2X There is a 0.77% of reference with a coverageData >= 3X There is a 0.48% of reference with a coverageData >= 4X There is a 0.29% of reference with a coverageData >= 5X There is a 0.18% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.04% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% 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 0.01% 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 16852573 0.0676129629382147 0.9001742899938489 chr2 243199373 15242439 0.06267466405022351 0.7241024218305342 chr3 198022430 9372444 0.04733021405706414 0.4462147998224652 chr4 191154276 9428850 0.04932586493644537 0.4644134094763797 chr5 180915260 9535474 0.05270685292108582 0.4720473166283777 chr6 171115067 11011390 0.06435079150569482 0.5846645456282342 chr7 159138663 14011104 0.08804336881980716 1.0578234163406224 chr8 146364022 9134276 0.06240793246307484 1.0386829810139457 chr9 141213431 6499754 0.046027873935022515 0.6132613329776688 chr10 135534747 8140074 0.060058945622261724 0.5693619928800474 chr11 135006516 9052151 0.06704973410320432 0.617149068306512 chr12 133851895 7494105 0.05598803812228433 0.49515290329598827 chr13 115169878 5528681 0.04800457459892421 0.45808032658322906 chr14 107349540 4507689 0.04199076214020107 0.45369957246565434 chr15 102531392 4112442 0.04010910141549624 0.4228523475554125 chr16 90354753 4100479 0.04538199556585584 0.45944167387659746 chr17 81195210 4671943 0.05753963811412028 0.5093963082373816 chr18 78077248 3507909 0.044928696769640245 1.065061748425418 chr19 59128983 2624781 0.04439076856775974 0.6019130635188605 chr20 63025520 3031743 0.04810341905945401 0.4522340586898476 chr21 48129895 1714945 0.03563159653683018 0.4078031866783579 chr22 51304566 1277433 0.024899011912506968 0.31415334206119194 chrMT 16571 21754 1.3127753303964758 2.4364951647028246 chrX 155270560 10641376 0.06853440858331418 0.564986090654107 chrY 59373566 469948 0.007915104846490103 0.1771114678651109