BamQC report ----------------------------------- >>>>>>> Input bam file = SRR618578.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 = 63,651,058 number of mapped reads = 58,957,362 (92.63%) number of supplementary alignments = 143,433 (0.23%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 29,740,319 number of mapped paired reads (second in pair) = 29,217,043 number of mapped paired reads (both in pair) = 57,856,318 number of mapped paired reads (singletons) = 1,101,044 number of mapped bases = 5,570,999,217 bp number of sequenced bases = 5,567,161,315 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 11,518,019 duplication rate = 16.83% >>>>>>> Insert size mean insert size = 45,322.6645 std insert size = 2,113,936.0928 median insert size = 199 >>>>>>> Mapping quality mean mapping quality = 52.5316 >>>>>>> ACTG content number of A's = 1,504,102,112 bp (27.02%) number of C's = 1,232,802,768 bp (22.14%) number of T's = 1,522,116,908 bp (27.34%) number of G's = 1,307,975,439 bp (23.49%) number of N's = 164,088 bp (0%) GC percentage = 45.64% >>>>>>> Mismatches and indels general error rate = 0.0129 number of mismatches = 70,186,774 number of insertions = 1,000,543 mapped reads with insertion percentage = 1.67% number of deletions = 2,804,520 mapped reads with deletion percentage = 4.64% homopolymer indels = 52.69% >>>>>>> Coverage mean coverageData = 1.7996X std coverageData = 7.5036X There is a 29.52% of reference with a coverageData >= 1X There is a 20.59% of reference with a coverageData >= 2X There is a 15.62% of reference with a coverageData >= 3X There is a 12.52% of reference with a coverageData >= 4X There is a 10.31% of reference with a coverageData >= 5X There is a 8.69% of reference with a coverageData >= 6X There is a 7.43% of reference with a coverageData >= 7X There is a 6.44% of reference with a coverageData >= 8X There is a 5.63% of reference with a coverageData >= 9X There is a 4.97% of reference with a coverageData >= 10X There is a 4.41% of reference with a coverageData >= 11X There is a 3.94% of reference with a coverageData >= 12X There is a 3.53% of reference with a coverageData >= 13X There is a 3.19% of reference with a coverageData >= 14X There is a 2.88% of reference with a coverageData >= 15X There is a 2.62% of reference with a coverageData >= 16X There is a 2.39% of reference with a coverageData >= 17X There is a 2.18% of reference with a coverageData >= 18X There is a 2% of reference with a coverageData >= 19X There is a 1.84% of reference with a coverageData >= 20X There is a 1.69% of reference with a coverageData >= 21X There is a 1.56% of reference with a coverageData >= 22X There is a 1.44% of reference with a coverageData >= 23X There is a 1.33% of reference with a coverageData >= 24X There is a 1.24% of reference with a coverageData >= 25X There is a 1.15% of reference with a coverageData >= 26X There is a 1.07% of reference with a coverageData >= 27X There is a 0.99% of reference with a coverageData >= 28X There is a 0.93% of reference with a coverageData >= 29X There is a 0.87% of reference with a coverageData >= 30X There is a 0.81% of reference with a coverageData >= 31X There is a 0.76% of reference with a coverageData >= 32X There is a 0.71% of reference with a coverageData >= 33X There is a 0.67% of reference with a coverageData >= 34X There is a 0.63% of reference with a coverageData >= 35X There is a 0.59% of reference with a coverageData >= 36X There is a 0.55% of reference with a coverageData >= 37X There is a 0.52% of reference with a coverageData >= 38X There is a 0.49% of reference with a coverageData >= 39X There is a 0.46% of reference with a coverageData >= 40X There is a 0.44% of reference with a coverageData >= 41X There is a 0.41% of reference with a coverageData >= 42X There is a 0.39% of reference with a coverageData >= 43X There is a 0.37% of reference with a coverageData >= 44X There is a 0.35% of reference with a coverageData >= 45X There is a 0.33% of reference with a coverageData >= 46X There is a 0.31% of reference with a coverageData >= 47X There is a 0.3% of reference with a coverageData >= 48X There is a 0.28% of reference with a coverageData >= 49X There is a 0.27% of reference with a coverageData >= 50X There is a 0.26% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 509865657 2.0455943297328836 9.23075297044981 chr2 243199373 490412648 2.0165045738008542 9.193623627044605 chr3 198022430 366835037 1.8524923514977572 5.70042825122842 chr4 191154276 288510429 1.5093066973819618 5.61986719042881 chr5 180915260 324023142 1.791021619735118 5.591850197616759 chr6 171115067 316125215 1.847442312020367 6.2358934853978765 chr7 159138663 292971302 1.8409812956641467 5.949950142611377 chr8 146364022 283275461 1.9354173049439705 6.1271511133632375 chr9 141213431 251969410 1.784316181652721 7.523256528425769 chr10 135534747 289567667 2.1364828828728326 6.714978658462781 chr11 135006516 292803634 2.1688111261237197 8.794635790111924 chr12 133851895 254058089 1.8980537331951857 6.146794944301307 chr13 115169878 152964372 1.3281630115124372 4.890855049707675 chr14 107349540 181082901 1.6868530689558614 5.894904278389183 chr15 102531392 187603712 1.829719740857512 6.23174284934046 chr16 90354753 206394234 2.284265377826886 17.42523399149567 chr17 81195210 192639744 2.3725505975044587 8.008856532804652 chr18 78077248 144696225 1.8532444304389417 7.0617536029666566 chr19 59128983 129592422 2.191690359362345 8.255167363302357 chr20 63025520 163764859 2.5983896523186165 7.809006059447933 chr21 48129895 76999269 1.5998220856289007 9.13428004216544 chr22 51304566 111186383 2.167182994979433 8.109176480146674 chrMT 16571 13806 0.8331422364371492 2.50996798915026 chrX 155270560 11068435 0.07128482694980942 1.833419806024386 chrY 59373566 52575164 0.8854978324865985 7.65063498540745