BamQC report ----------------------------------- >>>>>>> Input bam file = SRR504418.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP013494//SRP013494.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 = 139,823,618 number of mapped reads = 138,769,075 (99.25%) number of supplementary alignments = 2,305,875 (1.65%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 69,426,425 number of mapped paired reads (second in pair) = 69,342,650 number of mapped paired reads (both in pair) = 138,439,708 number of mapped paired reads (singletons) = 329,367 number of mapped bases = 13,301,003,558 bp number of sequenced bases = 13,296,676,701 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 66,638,813 duplication rate = 31.15% >>>>>>> Insert size mean insert size = 68,270.8774 std insert size = 2,405,724.0709 median insert size = 162 >>>>>>> Mapping quality mean mapping quality = 50.5744 >>>>>>> ACTG content number of A's = 4,004,709,307 bp (30.12%) number of C's = 2,631,934,436 bp (19.79%) number of T's = 4,025,638,070 bp (30.28%) number of G's = 2,632,328,288 bp (19.8%) number of N's = 2,066,600 bp (0.02%) GC percentage = 39.59% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 71,774,467 number of insertions = 1,317,870 mapped reads with insertion percentage = 0.94% number of deletions = 2,663,525 mapped reads with deletion percentage = 1.89% homopolymer indels = 47.99% >>>>>>> Coverage mean coverageData = 4.2966X std coverageData = 98.2711X There is a 26.68% of reference with a coverageData >= 1X There is a 20.57% of reference with a coverageData >= 2X There is a 16.15% of reference with a coverageData >= 3X There is a 13.68% of reference with a coverageData >= 4X There is a 11.78% of reference with a coverageData >= 5X There is a 10.39% of reference with a coverageData >= 6X There is a 9.28% of reference with a coverageData >= 7X There is a 8.39% of reference with a coverageData >= 8X There is a 7.66% of reference with a coverageData >= 9X There is a 7.03% of reference with a coverageData >= 10X There is a 6.5% of reference with a coverageData >= 11X There is a 6.04% of reference with a coverageData >= 12X There is a 5.63% of reference with a coverageData >= 13X There is a 5.28% of reference with a coverageData >= 14X There is a 4.96% of reference with a coverageData >= 15X There is a 4.68% of reference with a coverageData >= 16X There is a 4.42% of reference with a coverageData >= 17X There is a 4.19% of reference with a coverageData >= 18X There is a 3.98% of reference with a coverageData >= 19X There is a 3.79% of reference with a coverageData >= 20X There is a 3.62% of reference with a coverageData >= 21X There is a 3.46% of reference with a coverageData >= 22X There is a 3.31% of reference with a coverageData >= 23X There is a 3.17% of reference with a coverageData >= 24X There is a 3.04% of reference with a coverageData >= 25X There is a 2.92% of reference with a coverageData >= 26X There is a 2.81% of reference with a coverageData >= 27X There is a 2.71% of reference with a coverageData >= 28X There is a 2.61% of reference with a coverageData >= 29X There is a 2.52% of reference with a coverageData >= 30X There is a 2.44% of reference with a coverageData >= 31X There is a 2.36% of reference with a coverageData >= 32X There is a 2.28% of reference with a coverageData >= 33X There is a 2.21% of reference with a coverageData >= 34X There is a 2.14% of reference with a coverageData >= 35X There is a 2.08% of reference with a coverageData >= 36X There is a 2.01% of reference with a coverageData >= 37X There is a 1.96% of reference with a coverageData >= 38X There is a 1.9% of reference with a coverageData >= 39X There is a 1.85% of reference with a coverageData >= 40X There is a 1.8% of reference with a coverageData >= 41X There is a 1.75% of reference with a coverageData >= 42X There is a 1.7% of reference with a coverageData >= 43X There is a 1.66% of reference with a coverageData >= 44X There is a 1.62% of reference with a coverageData >= 45X There is a 1.58% of reference with a coverageData >= 46X There is a 1.54% of reference with a coverageData >= 47X There is a 1.5% of reference with a coverageData >= 48X There is a 1.47% of reference with a coverageData >= 49X There is a 1.43% of reference with a coverageData >= 50X There is a 1.4% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1046640801 4.199150223982792 42.795349775412895 chr2 243199373 1079155045 4.437326592120778 33.19967444666566 chr3 198022430 933016409 4.711670334517155 38.89386666725927 chr4 191154276 927226471 4.850670831972391 32.03120134651154 chr5 180915260 984123297 5.439692024873966 71.38471728459146 chr6 171115067 823554793 4.812871288534749 61.13855527339706 chr7 159138663 733768396 4.61087445481429 54.227483388865096 chr8 146364022 824792395 5.635212695917853 74.64868095605154 chr9 141213431 468100233 3.314842148407257 24.35641037460034 chr10 135534747 628015220 4.633610449724748 62.51598288261957 chr11 135006516 707805675 5.242751949839221 45.1806586017155 chr12 133851895 796206639 5.948415141974643 99.7913199920384 chr13 115169878 434973482 3.7767990168401497 34.941537900164626 chr14 107349540 891255702 8.302370946349654 450.6530899779521 chr15 102531392 367712547 3.5863411178500337 29.127876012720865 chr16 90354753 280616070 3.105714538337568 46.66195606573065 chr17 81195210 201147675 2.477334254077303 21.63568608544701 chr18 78077248 341734278 4.37687401584646 62.17815882273495 chr19 59128983 131501389 2.223975152760534 36.052632611318764 chr20 63025520 266005491 4.220599703104393 99.21780238231419 chr21 48129895 119330953 2.4793520326607816 17.101334966793722 chr22 51304566 98925673 1.9282040705694694 28.942032967212043 chrMT 16571 549 0.0331301671594955 0.4199775231153677 chrX 155270560 27004335 0.1739179339599213 3.5203005363084965 chrY 59373566 188390040 3.1729615162410827 68.62859663144474