BamQC report ----------------------------------- >>>>>>> Input bam file = SRR089750.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 26,210,053 number of mapped reads = 22,697,810 (86.6%) number of supplementary alignments = 1,091 (0%) number of secondary alignments = 0 number of mapped bases = 1,077,350,011 bp number of sequenced bases = 1,077,132,317 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,477,443 duplication rate = 11.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.1639 >>>>>>> ACTG content number of A's = 326,539,447 bp (30.32%) number of C's = 213,313,998 bp (19.8%) number of T's = 312,665,638 bp (29.03%) number of G's = 224,591,495 bp (20.85%) number of N's = 21,739 bp (0%) GC percentage = 40.65% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 3,847,355 number of insertions = 41,727 mapped reads with insertion percentage = 0.18% number of deletions = 142,194 mapped reads with deletion percentage = 0.63% homopolymer indels = 48.99% >>>>>>> Coverage mean coverageData = 0.348X std coverageData = 2.5905X There is a 13.3% of reference with a coverageData >= 1X There is a 7.58% of reference with a coverageData >= 2X There is a 4.67% of reference with a coverageData >= 3X There is a 2.96% of reference with a coverageData >= 4X There is a 1.89% of reference with a coverageData >= 5X There is a 1.23% of reference with a coverageData >= 6X There is a 0.8% of reference with a coverageData >= 7X There is a 0.53% of reference with a coverageData >= 8X There is a 0.36% of reference with a coverageData >= 9X There is a 0.25% of reference with a coverageData >= 10X There is a 0.17% of reference with a coverageData >= 11X There is a 0.12% of reference with a coverageData >= 12X There is a 0.09% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.05% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% 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 85064040 0.3412791497117273 5.297097451334684 chr2 243199373 88251446 0.362876947055287 2.1329907799268475 chr3 198022430 74233272 0.3748730484723372 1.2763830086561958 chr4 191154276 72565979 0.3796199620457352 1.4635737552059167 chr5 180915260 66148687 0.3656335402552554 1.2890004851230514 chr6 171115067 64006993 0.37405819441954813 1.544588484643486 chr7 159138663 60765149 0.381837749887342 3.064239496939258 chr8 146364022 56566711 0.3864796158717202 4.913471388754315 chr9 141213431 47948465 0.3395460662661755 2.0543386997693633 chr10 135534747 49216570 0.36312879973133383 2.1372107051605784 chr11 135006516 46925527 0.3475797197818215 2.044305610606682 chr12 133851895 49376336 0.36888783681396514 1.4160227352738444 chr13 115169878 33123249 0.28760340442489657 1.1069977502940374 chr14 107349540 31323428 0.29178912177918975 1.25407885190816 chr15 102531392 29264360 0.2854185379634756 1.104815924502116 chr16 90354753 30188504 0.3341108574553903 1.3453975029765932 chr17 81195210 27557637 0.33939978725345993 1.5486122302914336 chr18 78077248 28559415 0.3657840885990244 4.736861479781349 chr19 59128983 19447824 0.3289050988751151 3.4426319692616834 chr20 63025520 21339280 0.33858157774818837 1.356234878748024 chr21 48129895 14622451 0.3038122356178005 1.5078694779547626 chr22 51304566 11743195 0.22889181052618202 0.9650080727542975 chrMT 16571 350436 21.14754691931688 15.053321020927237 chrX 155270560 65366998 0.42098771331796575 1.7621683636859944 chrY 59373566 3394059 0.057164479559809495 1.5176394689220327