BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054614.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 = 15,536,473 number of mapped reads = 12,863,092 (82.79%) number of supplementary alignments = 359 (0%) number of secondary alignments = 0 number of mapped bases = 608,105,739 bp number of sequenced bases = 607,980,329 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 3,642,579 duplication rate = 19.37% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.285 >>>>>>> ACTG content number of A's = 179,046,977 bp (29.45%) number of C's = 119,334,790 bp (19.63%) number of T's = 179,832,325 bp (29.58%) number of G's = 129,662,736 bp (21.33%) number of N's = 103,501 bp (0.02%) GC percentage = 40.95% >>>>>>> Mismatches and indels general error rate = 0.0048 number of mismatches = 2,875,517 number of insertions = 23,613 mapped reads with insertion percentage = 0.18% number of deletions = 83,510 mapped reads with deletion percentage = 0.65% homopolymer indels = 46.72% >>>>>>> Coverage mean coverageData = 0.1964X std coverageData = 1.4587X There is a 6.82% of reference with a coverageData >= 1X There is a 3.21% of reference with a coverageData >= 2X There is a 2.02% of reference with a coverageData >= 3X There is a 1.41% of reference with a coverageData >= 4X There is a 1.04% of reference with a coverageData >= 5X There is a 0.79% of reference with a coverageData >= 6X There is a 0.62% of reference with a coverageData >= 7X There is a 0.5% of reference with a coverageData >= 8X There is a 0.41% of reference with a coverageData >= 9X There is a 0.34% of reference with a coverageData >= 10X There is a 0.28% of reference with a coverageData >= 11X There is a 0.24% of reference with a coverageData >= 12X There is a 0.2% of reference with a coverageData >= 13X There is a 0.17% of reference with a coverageData >= 14X There is a 0.15% of reference with a coverageData >= 15X There is a 0.13% of reference with a coverageData >= 16X There is a 0.11% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% of reference with a coverageData >= 20X There is a 0.07% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 55676325 0.22337486974606174 1.6767370499966747 chr2 243199373 52451332 0.21567215142450225 1.598863912283292 chr3 198022430 42908209 0.21668357973387156 1.470760710364667 chr4 191154276 37549179 0.19643389510156706 1.4221029141647537 chr5 180915260 31014275 0.17142984511090995 1.218621093522435 chr6 171115067 31791814 0.18579202029006597 1.419670988774032 chr7 159138663 39202357 0.2463408719224944 1.7309437014530236 chr8 146364022 29453274 0.20123301886306458 1.4558291795343208 chr9 141213431 28869287 0.20443726064555431 1.5171172426677695 chr10 135534747 27180101 0.20053972580182705 1.4498193921791482 chr11 135006516 25348264 0.18775585616919407 1.3962560487028606 chr12 133851895 21971804 0.16415011531962248 1.1997803717583584 chr13 115169878 20455479 0.1776113629294632 1.287152763070826 chr14 107349540 14387756 0.13402717887752477 1.1803461812789267 chr15 102531392 16341837 0.1593837426882881 1.162291055265843 chr16 90354753 17660485 0.19545717755434514 1.4540233401833103 chr17 81195210 12210506 0.150384560862642 1.0995268977754988 chr18 78077248 23722270 0.3038307651417222 1.9672211258809111 chr19 59128983 11990731 0.20278940025063513 1.5310836064678304 chr20 63025520 12262211 0.19455945781962608 1.453112715749216 chr21 48129895 8272051 0.17186929246365487 1.558432078020114 chr22 51304566 6325228 0.12328781808621088 1.0231427348201143 chrMT 16571 41716 2.517409933015509 6.082132031987824 chrX 155270560 39529507 0.25458468752865965 1.6902343881306348 chrY 59373566 1489741 0.025090980723643918 0.5991063634260672