BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124874.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,821,730 number of mapped reads = 4,770,822 (98.94%) number of supplementary alignments = 19,330 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,386,709 number of mapped paired reads (second in pair) = 2,384,113 number of mapped paired reads (both in pair) = 4,754,274 number of mapped paired reads (singletons) = 16,548 number of mapped bases = 429,308,597 bp number of sequenced bases = 429,083,589 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 289,657 duplication rate = 3.88% >>>>>>> Insert size mean insert size = 41,950.0933 std insert size = 1,893,356.4141 median insert size = 191 >>>>>>> Mapping quality mean mapping quality = 53.2168 >>>>>>> ACTG content number of A's = 122,778,243 bp (28.61%) number of C's = 81,678,372 bp (19.04%) number of T's = 127,835,661 bp (29.79%) number of G's = 96,784,957 bp (22.56%) number of N's = 6,356 bp (0%) GC percentage = 41.59% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 3,124,081 number of insertions = 54,451 mapped reads with insertion percentage = 1.11% number of deletions = 136,630 mapped reads with deletion percentage = 2.81% homopolymer indels = 47.01% >>>>>>> Coverage mean coverageData = 0.1387X std coverageData = 1.3552X There is a 9.37% of reference with a coverageData >= 1X There is a 2.6% of reference with a coverageData >= 2X There is a 0.76% of reference with a coverageData >= 3X There is a 0.3% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% 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 35633738 0.1429634873407196 1.371046168798211 chr2 243199373 42688932 0.17553060056614536 1.3951170366721706 chr3 198022430 36159656 0.18260383937314575 0.6049865484095833 chr4 191154276 23845994 0.12474737420992874 0.9282526247615626 chr5 180915260 18332859 0.10133395601896711 0.43799403560563593 chr6 171115067 24532908 0.14337082309648397 1.6804497332924206 chr7 159138663 28262085 0.17759408346920696 1.6646607579165509 chr8 146364022 22069332 0.15078385861793275 0.6565778096444502 chr9 141213431 13364914 0.09464336292487646 1.601344709572469 chr10 135534747 20614776 0.15209956454930337 4.0074980319463 chr11 135006516 22536617 0.16692984655644325 0.9464792685568286 chr12 133851895 22093676 0.1650606141960112 0.5590401295662234 chr13 115169878 12648895 0.10982815315650504 0.4304877075866664 chr14 107349540 17509317 0.1631056546679194 0.5694578092074879 chr15 102531392 12437296 0.12130232270717635 0.4688993681745783 chr16 90354753 11988949 0.1326875300074142 1.2749387487829107 chr17 81195210 12001294 0.14780790640236044 1.0500511854078316 chr18 78077248 7809656 0.10002473447834637 1.5063588884535337 chr19 59128983 6228392 0.10533568622345492 0.9434496076225455 chr20 63025520 11444120 0.1815791444481537 0.649942034446375 chr21 48129895 3263654 0.0678092898395062 0.5104834888601655 chr22 51304566 4605058 0.08975922337984499 0.42611876043659347 chrMT 16571 42555 2.5680405527729167 1.802103746554889 chrX 155270560 17989409 0.11585846666618578 0.6295108582349175 chrY 59373566 1204515 0.02028705838554484 1.4458218479144107