BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153336.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 64,492,272 number of mapped reads = 63,864,279 (99.03%) number of supplementary alignments = 311,640 (0.48%) number of secondary alignments = 0 number of mapped bases = 6,255,008,970 bp number of sequenced bases = 6,254,246,338 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 45,136,449 duplication rate = 60.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.5864 >>>>>>> ACTG content number of A's = 1,644,015,552 bp (26.29%) number of C's = 1,472,342,942 bp (23.54%) number of T's = 1,688,686,463 bp (27%) number of G's = 1,447,087,235 bp (23.14%) number of N's = 2,114,146 bp (0.03%) GC percentage = 46.68% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 18,639,914 number of insertions = 413,134 mapped reads with insertion percentage = 0.64% number of deletions = 381,018 mapped reads with deletion percentage = 0.59% homopolymer indels = 49.7% >>>>>>> Coverage mean coverageData = 2.0206X std coverageData = 21.6018X There is a 11.22% of reference with a coverageData >= 1X There is a 7.87% of reference with a coverageData >= 2X There is a 5.51% of reference with a coverageData >= 3X There is a 4.59% of reference with a coverageData >= 4X There is a 3.74% of reference with a coverageData >= 5X There is a 3.42% of reference with a coverageData >= 6X There is a 3.03% of reference with a coverageData >= 7X There is a 2.86% of reference with a coverageData >= 8X There is a 2.65% of reference with a coverageData >= 9X There is a 2.53% of reference with a coverageData >= 10X There is a 2.4% of reference with a coverageData >= 11X There is a 2.31% of reference with a coverageData >= 12X There is a 2.22% of reference with a coverageData >= 13X There is a 2.14% of reference with a coverageData >= 14X There is a 2.07% of reference with a coverageData >= 15X There is a 2% of reference with a coverageData >= 16X There is a 1.94% of reference with a coverageData >= 17X There is a 1.89% of reference with a coverageData >= 18X There is a 1.83% of reference with a coverageData >= 19X There is a 1.79% of reference with a coverageData >= 20X There is a 1.74% of reference with a coverageData >= 21X There is a 1.69% of reference with a coverageData >= 22X There is a 1.65% of reference with a coverageData >= 23X There is a 1.61% of reference with a coverageData >= 24X There is a 1.57% of reference with a coverageData >= 25X There is a 1.54% of reference with a coverageData >= 26X There is a 1.5% of reference with a coverageData >= 27X There is a 1.47% of reference with a coverageData >= 28X There is a 1.44% of reference with a coverageData >= 29X There is a 1.4% of reference with a coverageData >= 30X There is a 1.38% of reference with a coverageData >= 31X There is a 1.35% of reference with a coverageData >= 32X There is a 1.32% of reference with a coverageData >= 33X There is a 1.29% of reference with a coverageData >= 34X There is a 1.27% of reference with a coverageData >= 35X There is a 1.24% of reference with a coverageData >= 36X There is a 1.22% of reference with a coverageData >= 37X There is a 1.2% of reference with a coverageData >= 38X There is a 1.17% of reference with a coverageData >= 39X There is a 1.15% of reference with a coverageData >= 40X There is a 1.13% of reference with a coverageData >= 41X There is a 1.11% of reference with a coverageData >= 42X There is a 1.09% of reference with a coverageData >= 43X There is a 1.07% of reference with a coverageData >= 44X There is a 1.05% of reference with a coverageData >= 45X There is a 1.04% of reference with a coverageData >= 46X There is a 1.02% of reference with a coverageData >= 47X There is a 1% of reference with a coverageData >= 48X There is a 0.98% of reference with a coverageData >= 49X There is a 0.97% of reference with a coverageData >= 50X There is a 0.95% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 632194074 2.5363791330333334 23.460896466590277 chr2 243199373 459471167 1.8892777614192287 17.785312529377446 chr3 198022430 325705931 1.6447931226780723 16.004052600651864 chr4 191154276 250600265 1.3109843538106363 14.972565586315685 chr5 180915260 402479032 2.2246826055469286 22.56544444942692 chr6 171115067 216839633 1.267215311904708 13.472847897330935 chr7 159138663 321155927 2.0180886338098745 24.95661277333109 chr8 146364022 323921715 2.2131238987133055 37.07617385975754 chr9 141213431 162146382 1.1482362608978745 12.109739365176253 chr10 135534747 303322195 2.2379662906664075 20.739052586713548 chr11 135006516 291806947 2.161428615786219 19.380864931671365 chr12 133851895 314409677 2.348937062116304 20.870067494107175 chr13 115169878 85513752 0.7425010209700839 11.711455484529044 chr14 107349540 175063947 1.6307843238080013 15.578259568274918 chr15 102531392 296010300 2.887021176889903 24.936277400492944 chr16 90354753 291917378 3.2307916109294217 30.14763158733933 chr17 81195210 257673138 3.1735017127241867 22.429945337258946 chr18 78077248 72350628 0.9266544333119938 10.590856082980999 chr19 59128983 307178836 5.19506374733352 34.05796732190914 chr20 63025520 149574186 2.3732320812267793 21.106681284298624 chr21 48129895 66704064 1.3859175051181807 15.797226217479071 chr22 51304566 91232716 1.7782572412755622 17.9408695018736 chrMT 16571 12236 0.7383984068553497 2.43700373660387 chrX 155270560 454391618 2.9264505647432455 32.15404201141227 chrY 59373566 3333226 0.05613989902509814 2.173296095898314