BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472582.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 10,866,736 number of mapped reads = 9,735,337 (89.59%) number of supplementary alignments = 286,981 (2.64%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 4,912,850 number of mapped paired reads (second in pair) = 4,822,487 number of mapped paired reads (both in pair) = 9,483,228 number of mapped paired reads (singletons) = 252,109 number of mapped bases = 788,649,468 bp number of sequenced bases = 788,321,232 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,653,698 duplication rate = 13.94% >>>>>>> Insert size mean insert size = 219,934.1514 std insert size = 4,511,219.8152 median insert size = 128 >>>>>>> Mapping quality mean mapping quality = 50.286 >>>>>>> ACTG content number of A's = 201,925,269 bp (25.61%) number of C's = 156,686,859 bp (19.88%) number of T's = 236,003,699 bp (29.94%) number of G's = 193,180,445 bp (24.51%) number of N's = 524,960 bp (0.07%) GC percentage = 44.38% >>>>>>> Mismatches and indels general error rate = 0.0124 number of mismatches = 9,642,828 number of insertions = 76,596 mapped reads with insertion percentage = 0.77% number of deletions = 176,375 mapped reads with deletion percentage = 1.77% homopolymer indels = 41.98% >>>>>>> Coverage mean coverageData = 0.2548X std coverageData = 3.1482X There is a 13.06% of reference with a coverageData >= 1X There is a 6.22% of reference with a coverageData >= 2X There is a 2.45% of reference with a coverageData >= 3X There is a 1.26% of reference with a coverageData >= 4X There is a 0.63% of reference with a coverageData >= 5X There is a 0.36% of reference with a coverageData >= 6X There is a 0.21% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.08% of reference with a coverageData >= 9X There is a 0.06% of reference with a coverageData >= 10X There is a 0.04% of reference with a coverageData >= 11X There is a 0.03% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.02% of reference with a coverageData >= 14X There is a 0.02% 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 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% 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 51977227 0.20853399197749642 3.7592057764477347 chr2 243199373 76077777 0.31282061323406457 4.196287643241744 chr3 198022430 42756043 0.21591515163206512 0.7378689967172619 chr4 191154276 41894216 0.21916441984274523 1.4953878259252047 chr5 180915260 39247822 0.2169403620236347 0.8104902503656642 chr6 171115067 52754409 0.3082978601761585 1.5521935656369747 chr7 159138663 64088105 0.4027186341260137 4.917691200812586 chr8 146364022 39340724 0.26878684708459294 2.560206782370735 chr9 141213431 27698975 0.19614972034777628 3.1575715832729623 chr10 135534747 30146523 0.22242652653492614 2.482492617274708 chr11 135006516 29129071 0.21576048225701935 2.0984167692139466 chr12 133851895 38935456 0.29088460794671606 0.9151989528693337 chr13 115169878 39170968 0.3401146956151156 0.9949762862815607 chr14 107349540 21256806 0.19801487738093707 9.56655188716744 chr15 102531392 18499437 0.18042705398947476 0.69576312714824 chr16 90354753 29254426 0.32377296189388066 1.48573742683019 chr17 81195210 27515257 0.33887783528116994 2.4574266087171948 chr18 78077248 18547653 0.23755515819410028 5.3673340852650355 chr19 59128983 14950787 0.2528503999468416 2.6279020106758617 chr20 63025520 26652173 0.4228790654960086 2.08789754602616 chr21 48129895 12104317 0.25149269492484866 1.103636096373705 chr22 51304566 7697923 0.1500436237975388 0.6339561872963682 chrMT 16571 54020 3.2599118942731278 3.971617048990627 chrX 155270560 37108663 0.23899355421916427 1.301166630878949 chrY 59373566 1790690 0.030159717878491584 1.1999592107019246