BamQC report ----------------------------------- >>>>>>> Input bam file = SRR975322.sorted.bam outfile = /mainsd/zhouyj/SRP029757/SRP029757.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 = 4,099,056 number of mapped reads = 4,053,995 (98.9%) number of supplementary alignments = 30,210 (0.74%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,026,231 number of mapped paired reads (second in pair) = 2,027,764 number of mapped paired reads (both in pair) = 4,038,856 number of mapped paired reads (singletons) = 15,139 number of mapped bases = 382,835,971 bp number of sequenced bases = 382,589,872 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 312,714 duplication rate = 3.79% >>>>>>> Insert size mean insert size = 91,712.5649 std insert size = 2,884,149.4736 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 52.5737 >>>>>>> ACTG content number of A's = 113,110,040 bp (29.56%) number of C's = 77,436,949 bp (20.24%) number of T's = 111,405,466 bp (29.12%) number of G's = 80,629,660 bp (21.07%) number of N's = 7,757 bp (0%) GC percentage = 41.31% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 3,068,718 number of insertions = 74,145 mapped reads with insertion percentage = 1.79% number of deletions = 140,318 mapped reads with deletion percentage = 3.38% homopolymer indels = 47.08% >>>>>>> Coverage mean coverageData = 0.1237X std coverageData = 2.1614X There is a 8.27% of reference with a coverageData >= 1X There is a 2.44% of reference with a coverageData >= 2X There is a 0.59% of reference with a coverageData >= 3X There is a 0.19% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 0.01% 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% 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 37215562 0.1493098065340427 1.8674120140955957 chr2 243199373 22520804 0.09260222887170026 1.5039043175474875 chr3 198022430 15959677 0.08059529922948627 0.5868814222331732 chr4 191154276 23036281 0.12051146059636145 1.6417990002161726 chr5 180915260 21111351 0.11669193079677193 0.45266654582188226 chr6 171115067 24604317 0.1437881387733086 1.4981814960366102 chr7 159138663 18236306 0.11459381181303503 1.9364824322995133 chr8 146364022 29128915 0.1990169073107324 0.7937039690497731 chr9 141213431 14581084 0.1032556457041257 1.6902105513182963 chr10 135534747 23037153 0.16997230237940386 8.201981077371228 chr11 135006516 16742918 0.12401562899378872 1.5293184509599562 chr12 133851895 19869552 0.14844430853967364 0.5012575600653743 chr13 115169878 10954021 0.09511185728615602 0.3931097250631919 chr14 107349540 20119433 0.18741983430949027 0.6067753123414218 chr15 102531392 6436394 0.06277486216123936 0.3141591526996347 chr16 90354753 8912300 0.09863675904243797 1.6848957159757545 chr17 81195210 10674696 0.13146952880594803 2.193618440849256 chr18 78077248 18497400 0.23691152638986457 2.329948420785788 chr19 59128983 4335083 0.07331570373872319 1.0092107203476308 chr20 63025520 5132514 0.08143548835455859 0.5270369136338992 chr21 48129895 5723346 0.11891457481883141 0.7620300313317614 chr22 51304566 3650923 0.07116175585619416 0.3574588363572389 chrMT 16571 98624 5.951602196608533 5.239977737515931 chrX 155270560 20914877 0.13469956571290784 0.8120569635646243 chrY 59373566 1342440 0.022610061858167656 1.4151080941445295