BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1506328.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 = 7,355,470 number of mapped reads = 5,338,437 (72.58%) number of supplementary alignments = 81,075 (1.1%) number of secondary alignments = 0 number of mapped bases = 425,653,132 bp number of sequenced bases = 425,459,779 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 932,405 duplication rate = 11.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.5553 >>>>>>> ACTG content number of A's = 120,462,278 bp (28.31%) number of C's = 79,867,729 bp (18.77%) number of T's = 116,745,635 bp (27.44%) number of G's = 108,281,217 bp (25.45%) number of N's = 102,920 bp (0.02%) GC percentage = 44.22% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 3,065,253 number of insertions = 36,874 mapped reads with insertion percentage = 0.67% number of deletions = 92,992 mapped reads with deletion percentage = 1.71% homopolymer indels = 42.11% >>>>>>> Coverage mean coverageData = 0.1375X std coverageData = 0.9707X There is a 7.86% of reference with a coverageData >= 1X There is a 2.89% of reference with a coverageData >= 2X There is a 1.26% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.33% of reference with a coverageData >= 5X There is a 0.19% of reference with a coverageData >= 6X There is a 0.11% of reference with a coverageData >= 7X There is a 0.07% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.04% of reference with a coverageData >= 10X There is a 0.03% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% 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% 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 33174591 0.1330973253623308 1.5819702200818697 chr2 243199373 34099207 0.14021091657995352 1.0277547621900478 chr3 198022430 26187808 0.1322466752882489 0.58408409590527 chr4 191154276 25259825 0.13214365657193042 1.019400878344683 chr5 180915260 32501223 0.17964887539061106 0.6903749251866403 chr6 171115067 15206455 0.0888668383597103 0.5035167816245625 chr7 159138663 22067404 0.13866777302257466 1.1121658411533306 chr8 146364022 25886829 0.17686606753673387 1.2507479174950562 chr9 141213431 11657912 0.0825552634579072 0.8252209918212898 chr10 135534747 23747178 0.1752109958931786 1.2525668329918285 chr11 135006516 17723297 0.13127734516162168 0.8736489846061826 chr12 133851895 18134956 0.13548523911447052 0.6278026469640878 chr13 115169878 8964378 0.07783613350706163 0.44525382922166934 chr14 107349540 12145881 0.11314329805232515 0.5987942721279419 chr15 102531392 16217197 0.1581681149905777 0.6695295428232649 chr16 90354753 15968575 0.1767319866393747 0.9015371159241291 chr17 81195210 11238445 0.13841266005716346 0.6978995185392176 chr18 78077248 7688182 0.09846891632246055 1.2637150832448851 chr19 59128983 11173244 0.18896391301030832 1.29409820534547 chr20 63025520 12217869 0.19385590154591348 0.8191837440964496 chr21 48129895 7566350 0.15720686695867506 0.8831722561060216 chr22 51304566 5385451 0.1049702086944854 0.5698620222519168 chrMT 16571 51930 3.1337879427916238 6.7551336613031046 chrX 155270560 29559520 0.1903742731397375 0.7896872865042166 chrY 59373566 1829425 0.030812112582222197 1.3476930618435508