BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081115.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,506,692 number of mapped reads = 2,300,145 (91.76%) number of supplementary alignments = 14,497 (0.58%) number of secondary alignments = 0 number of mapped bases = 159,699,449 bp number of sequenced bases = 159,634,902 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 87,850 duplication rate = 2.86% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.1745 >>>>>>> ACTG content number of A's = 46,470,383 bp (29.11%) number of C's = 30,218,270 bp (18.93%) number of T's = 49,860,865 bp (31.23%) number of G's = 33,083,610 bp (20.72%) number of N's = 1,774 bp (0%) GC percentage = 39.65% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,391,625 number of insertions = 12,717 mapped reads with insertion percentage = 0.55% number of deletions = 35,908 mapped reads with deletion percentage = 1.54% homopolymer indels = 47.39% >>>>>>> Coverage mean coverageData = 0.0516X std coverageData = 0.4423X There is a 4.23% of reference with a coverageData >= 1X There is a 0.65% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% 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 13625847 0.05466725396844648 0.6873561292544642 chr2 243199373 10400263 0.042764349561049235 0.44600636738813104 chr3 198022430 13505050 0.06819959738904326 0.30830306335816926 chr4 191154276 9787172 0.051200382250408044 0.3022344585853944 chr5 180915260 8131559 0.044946783372502686 0.2505282845415566 chr6 171115067 13532880 0.07908643135440552 0.4644989834149098 chr7 159138663 7742363 0.0486516780651852 0.42668238952747534 chr8 146364022 12720731 0.08691159771490838 0.6870976332218919 chr9 141213431 7681272 0.05439476929074827 0.5178875068241418 chr10 135534747 7659570 0.05651369976733715 0.42597926868371383 chr11 135006516 7229531 0.053549496825768025 0.3729156313525725 chr12 133851895 7584990 0.05666703485968577 0.2917437709257418 chr13 115169878 4045224 0.035123975732613 0.2159619748248617 chr14 107349540 4418213 0.041157260664554315 0.3183864120137947 chr15 102531392 4154508 0.040519375763473496 0.23666491958834412 chr16 90354753 4214992 0.04664936663597542 0.3302848727413767 chr17 81195210 3508559 0.04321140372689473 0.25721584913699663 chr18 78077248 3915202 0.05014523565174838 1.0489809631309988 chr19 59128983 3238985 0.05477829713391147 0.5103900570874434 chr20 63025520 2513840 0.03988606520025539 0.25153582370848676 chr21 48129895 3051171 0.06339450771708519 0.35359931680740303 chr22 51304566 1654233 0.03224338745989977 0.2064714268440818 chrMT 16571 149518 9.022871281153822 5.740709733000623 chrX 155270560 4827886 0.031093376619495672 0.2395687356834812 chrY 59373566 405890 0.0068362072104613016 0.18150799312384747