BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081746.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 = 2,150,668 number of mapped reads = 1,932,702 (89.87%) number of supplementary alignments = 12,533 (0.58%) number of secondary alignments = 0 number of mapped bases = 129,017,077 bp number of sequenced bases = 128,970,624 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 78,883 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8346 >>>>>>> ACTG content number of A's = 35,390,747 bp (27.44%) number of C's = 24,318,640 bp (18.86%) number of T's = 40,345,407 bp (31.28%) number of G's = 28,914,362 bp (22.42%) number of N's = 1,468 bp (0%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 1,034,116 number of insertions = 9,425 mapped reads with insertion percentage = 0.48% number of deletions = 26,094 mapped reads with deletion percentage = 1.34% homopolymer indels = 47.17% >>>>>>> Coverage mean coverageData = 0.0417X std coverageData = 0.372X There is a 3.6% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.06% 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 10241303 0.04108837506166133 0.6082243906883857 chr2 243199373 10970650 0.04510969689054256 0.4705673357133411 chr3 198022430 8694389 0.043906081750436046 0.2389680004568996 chr4 191154276 8647504 0.04523834978193216 0.2652049179439936 chr5 180915260 7947719 0.04393061701926084 0.23629556442199007 chr6 171115067 7534617 0.04403245799506364 0.2776277648214661 chr7 159138663 7180259 0.04511951316318399 0.5211996238027309 chr8 146364022 6550514 0.04475494667671814 0.4665932124324595 chr9 141213431 5395284 0.03820659240267309 0.35542558337634766 chr10 135534747 6231756 0.045979028536497726 0.43501995882958516 chr11 135006516 5787058 0.04286502734430981 0.31690825564377073 chr12 133851895 5817786 0.04346435289541474 0.23665107898387594 chr13 115169878 4109873 0.035685311744447626 0.21007586634754527 chr14 107349540 3905092 0.03637735196629627 0.23408093076278208 chr15 102531392 3614021 0.03524794630701981 0.21356866719253684 chr16 90354753 3648160 0.040375961184908556 0.2627068080529927 chr17 81195210 3314978 0.040827260622886496 0.24404801397589931 chr18 78077248 3439583 0.044053589081418446 0.6436260883999446 chr19 59128983 2521720 0.042647782391251346 0.4786482167484283 chr20 63025520 2552096 0.040493057415472336 0.23577924194342464 chr21 48129895 1708682 0.03550146951286721 0.23631281464379067 chr22 51304566 1348338 0.02628105264548968 0.1798547623960338 chrMT 16571 49958 3.014784865125822 2.6150160129849405 chrX 155270560 7408004 0.047710293567563615 0.27931694948459446 chrY 59373566 397733 0.006698822839780248 0.17063527523075703