BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618659.sorted.bam outfile = /mainsd2/zhouyj/SRP017186/SRP017186.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 = 49,244,433 number of mapped reads = 33,816,899 (68.67%) number of supplementary alignments = 151,970 (0.31%) number of secondary alignments = 0 number of mapped bases = 3,275,030,354 bp number of sequenced bases = 3,272,867,451 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 17,963,420 duplication rate = 34.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 51.6809 >>>>>>> ACTG content number of A's = 877,383,637 bp (26.81%) number of C's = 759,080,891 bp (23.19%) number of T's = 926,089,840 bp (28.3%) number of G's = 709,376,126 bp (21.67%) number of N's = 936,957 bp (0.03%) GC percentage = 44.87% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 26,242,919 number of insertions = 578,067 mapped reads with insertion percentage = 1.67% number of deletions = 1,468,712 mapped reads with deletion percentage = 4.23% homopolymer indels = 52.02% >>>>>>> Coverage mean coverageData = 1.0579X std coverageData = 18.6103X There is a 18.04% of reference with a coverageData >= 1X There is a 11.63% of reference with a coverageData >= 2X There is a 8.54% of reference with a coverageData >= 3X There is a 6.65% of reference with a coverageData >= 4X There is a 5.36% of reference with a coverageData >= 5X There is a 4.43% of reference with a coverageData >= 6X There is a 3.72% of reference with a coverageData >= 7X There is a 3.17% of reference with a coverageData >= 8X There is a 2.72% of reference with a coverageData >= 9X There is a 2.35% of reference with a coverageData >= 10X There is a 2.05% of reference with a coverageData >= 11X There is a 1.8% of reference with a coverageData >= 12X There is a 1.59% of reference with a coverageData >= 13X There is a 1.41% of reference with a coverageData >= 14X There is a 1.26% of reference with a coverageData >= 15X There is a 1.13% of reference with a coverageData >= 16X There is a 1.02% of reference with a coverageData >= 17X There is a 0.93% of reference with a coverageData >= 18X There is a 0.84% of reference with a coverageData >= 19X There is a 0.77% of reference with a coverageData >= 20X There is a 0.71% of reference with a coverageData >= 21X There is a 0.65% of reference with a coverageData >= 22X There is a 0.6% of reference with a coverageData >= 23X There is a 0.55% of reference with a coverageData >= 24X There is a 0.51% of reference with a coverageData >= 25X There is a 0.48% of reference with a coverageData >= 26X There is a 0.44% of reference with a coverageData >= 27X There is a 0.41% of reference with a coverageData >= 28X There is a 0.39% of reference with a coverageData >= 29X There is a 0.36% of reference with a coverageData >= 30X There is a 0.34% of reference with a coverageData >= 31X There is a 0.32% of reference with a coverageData >= 32X There is a 0.3% of reference with a coverageData >= 33X There is a 0.29% of reference with a coverageData >= 34X There is a 0.27% of reference with a coverageData >= 35X There is a 0.26% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.22% of reference with a coverageData >= 39X There is a 0.21% of reference with a coverageData >= 40X There is a 0.2% of reference with a coverageData >= 41X There is a 0.19% of reference with a coverageData >= 42X There is a 0.18% of reference with a coverageData >= 43X There is a 0.18% of reference with a coverageData >= 44X There is a 0.17% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 290670947 1.1661794294987935 22.3939223941665 chr2 243199373 286475104 1.1779434316222517 19.224975699793244 chr3 198022430 213911064 1.0802365368408013 23.997644558435983 chr4 191154276 159230514 0.8329947795674736 16.258549301227102 chr5 180915260 165966744 0.9173728296883303 14.173728172829465 chr6 171115067 176747404 1.0329154942270513 12.923831556385956 chr7 159138663 157612577 0.990410337932775 22.27681678709449 chr8 146364022 150380174 1.0274394755290341 16.326670891968227 chr9 141213431 131866150 0.9338074223265632 23.991674985307952 chr10 135534747 180583662 1.3323790835718312 19.715576518729062 chr11 135006516 151775234 1.1242067308810488 11.26501700590912 chr12 133851895 152297840 1.1378086204905802 18.6101402672608 chr13 115169878 99725711 0.8659009867145991 22.369461628729002 chr14 107349540 114429925 1.0659563608749512 19.152490667456636 chr15 102531392 106924897 1.042850339923211 18.015488485274247 chr16 90354753 125336723 1.3871624772191011 22.478855567255863 chr17 81195210 109115523 1.3438665039477082 18.31678659605322 chr18 78077248 71524613 0.9160749748761636 14.357074303097454 chr19 59128983 76469819 1.293271338693581 10.705106441207196 chr20 63025520 91735937 1.4555363763757918 10.944656564307387 chr21 48129895 41425586 0.860703851525128 11.93133837512822 chr22 51304566 62291456 1.2141503350793377 18.507815052857765 chrMT 16571 10598 0.6395510228712812 2.911542276068425 chrX 155270560 146869810 0.9458960539589732 16.81774638889662 chrY 59373566 11652342 0.19625471038744752 13.163621060063212