BamQC report ----------------------------------- >>>>>>> Input bam file = SRR927000.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 11,861,206 number of mapped reads = 11,549,701 (97.37%) number of supplementary alignments = 287,023 (2.42%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 5,786,676 number of mapped paired reads (second in pair) = 5,763,025 number of mapped paired reads (both in pair) = 11,356,920 number of mapped paired reads (singletons) = 192,781 number of mapped bases = 1,055,593,747 bp number of sequenced bases = 1,054,790,617 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 702,167 duplication rate = 5% >>>>>>> Insert size mean insert size = 241,077.2861 std insert size = 4,802,071.7453 median insert size = 183 >>>>>>> Mapping quality mean mapping quality = 52.8488 >>>>>>> ACTG content number of A's = 302,992,792 bp (28.73%) number of C's = 204,849,160 bp (19.42%) number of T's = 307,342,364 bp (29.14%) number of G's = 239,405,273 bp (22.7%) number of N's = 201,028 bp (0.02%) GC percentage = 42.12% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 10,098,643 number of insertions = 178,473 mapped reads with insertion percentage = 1.52% number of deletions = 548,956 mapped reads with deletion percentage = 4.63% homopolymer indels = 52.01% >>>>>>> Coverage mean coverageData = 0.341X std coverageData = 1.4036X There is a 20.01% of reference with a coverageData >= 1X There is a 7.86% of reference with a coverageData >= 2X There is a 3.07% of reference with a coverageData >= 3X There is a 1.36% of reference with a coverageData >= 4X There is a 0.63% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.16% of reference with a coverageData >= 7X There is a 0.09% of reference with a coverageData >= 8X There is a 0.05% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.01% 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 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 87892691 0.3526277713867762 1.726268897396303 chr2 243199373 92314780 0.37958477795911094 2.3715297490471765 chr3 198022430 70203526 0.3545231012466618 0.8692425559151351 chr4 191154276 63607797 0.3327563386549616 1.0048714295526622 chr5 180915260 64814863 0.35826089518374515 0.8713416834312253 chr6 171115067 59894849 0.3500267396090842 0.9959213991487295 chr7 159138663 56090630 0.3524638761103579 1.1970922411799394 chr8 146364022 54397570 0.3716594369072476 0.9776173067989604 chr9 141213431 48208170 0.341385161868916 1.4566049920079542 chr10 135534747 51625963 0.3809057392492864 2.863310875017309 chr11 135006516 49881336 0.3694735445213622 1.0936323340353487 chr12 133851895 48982337 0.3659442923837574 0.8981069693301879 chr13 115169878 32289669 0.2803655744082667 0.7656907859882413 chr14 107349540 32180792 0.2997757791975634 0.811465515758769 chr15 102531392 29700074 0.28966810476931787 0.7868889946805444 chr16 90354753 32033428 0.35452952873436555 1.905290905614198 chr17 81195210 26088490 0.3213057765353399 1.0480868831428738 chr18 78077248 27777823 0.3557735923274345 1.3533837463258624 chr19 59128983 16631091 0.2812680035440488 1.1296050177376515 chr20 63025520 23293423 0.3695871608834009 0.9266793748348336 chr21 48129895 13063725 0.27142641802979206 1.2378454424887166 chr22 51304566 12132704 0.23648390281675905 0.7791522853765986 chrMT 16571 413563 24.95703337155271 23.573397865006918 chrX 155270560 60132830 0.3872777299186658 1.0083718419400416 chrY 59373566 1941623 0.032701808747684115 1.346399214235473