BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1695948.sorted.bam outfile = /seu_share/home/tujing/220232460/out/SRP050588/SRP050588.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 = 344,762,632 number of mapped reads = 342,929,621 (99.47%) number of supplementary alignments = 3,024,478 (0.88%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 171,763,418 number of mapped paired reads (second in pair) = 171,166,203 number of mapped paired reads (both in pair) = 341,824,294 number of mapped paired reads (singletons) = 1,105,327 number of mapped bases = 34,055,342,179 bp number of sequenced bases = 34,047,439,669 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 37,926,616 duplication rate = 10.14% >>>>>>> Insert size mean insert size = 59,992.5819 std insert size = 2,371,860.5119 median insert size = 320 >>>>>>> Mapping quality mean mapping quality = 54.1229 >>>>>>> ACTG content number of A's = 9,799,768,395 bp (28.78%) number of C's = 7,141,836,548 bp (20.98%) number of T's = 9,754,197,838 bp (28.65%) number of G's = 7,343,725,075 bp (21.57%) number of N's = 7,911,813 bp (0.02%) GC percentage = 42.55% >>>>>>> Mismatches and indels general error rate = 0.0039 number of mismatches = 127,582,150 number of insertions = 3,400,469 mapped reads with insertion percentage = 0.97% number of deletions = 3,385,112 mapped reads with deletion percentage = 0.96% homopolymer indels = 45.22% >>>>>>> Coverage mean coverageData = 11.0009X std coverageData = 16.4549X There is a 91.35% of reference with a coverageData >= 1X There is a 89.42% of reference with a coverageData >= 2X There is a 86.32% of reference with a coverageData >= 3X There is a 82.11% of reference with a coverageData >= 4X There is a 76.97% of reference with a coverageData >= 5X There is a 71.22% of reference with a coverageData >= 6X There is a 65.16% of reference with a coverageData >= 7X There is a 59.04% of reference with a coverageData >= 8X There is a 53.07% of reference with a coverageData >= 9X There is a 47.41% of reference with a coverageData >= 10X There is a 42.14% of reference with a coverageData >= 11X There is a 37.32% of reference with a coverageData >= 12X There is a 32.96% of reference with a coverageData >= 13X There is a 29.05% of reference with a coverageData >= 14X There is a 25.56% of reference with a coverageData >= 15X There is a 22.48% of reference with a coverageData >= 16X There is a 19.76% of reference with a coverageData >= 17X There is a 17.38% of reference with a coverageData >= 18X There is a 15.29% of reference with a coverageData >= 19X There is a 13.46% of reference with a coverageData >= 20X There is a 11.85% of reference with a coverageData >= 21X There is a 10.45% of reference with a coverageData >= 22X There is a 9.23% of reference with a coverageData >= 23X There is a 8.16% of reference with a coverageData >= 24X There is a 7.23% of reference with a coverageData >= 25X There is a 6.41% of reference with a coverageData >= 26X There is a 5.69% of reference with a coverageData >= 27X There is a 5.07% of reference with a coverageData >= 28X There is a 4.51% of reference with a coverageData >= 29X There is a 4.03% of reference with a coverageData >= 30X There is a 3.6% of reference with a coverageData >= 31X There is a 3.23% of reference with a coverageData >= 32X There is a 2.9% of reference with a coverageData >= 33X There is a 2.6% of reference with a coverageData >= 34X There is a 2.35% of reference with a coverageData >= 35X There is a 2.12% of reference with a coverageData >= 36X There is a 1.92% of reference with a coverageData >= 37X There is a 1.74% of reference with a coverageData >= 38X There is a 1.58% of reference with a coverageData >= 39X There is a 1.43% of reference with a coverageData >= 40X There is a 1.31% of reference with a coverageData >= 41X There is a 1.19% of reference with a coverageData >= 42X There is a 1.09% of reference with a coverageData >= 43X There is a 1% of reference with a coverageData >= 44X There is a 0.92% of reference with a coverageData >= 45X There is a 0.84% of reference with a coverageData >= 46X There is a 0.77% of reference with a coverageData >= 47X There is a 0.71% of reference with a coverageData >= 48X There is a 0.66% of reference with a coverageData >= 49X There is a 0.61% of reference with a coverageData >= 50X There is a 0.57% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2943028516 11.807507255919736 22.71851925080016 chr2 243199373 3014306654 12.394384972365863 27.869760314139977 chr3 198022430 2277113107 11.49926857780707 8.702557022053115 chr4 191154276 2006511347 10.496816440559247 14.374667881593481 chr5 180915260 2023504708 11.184820495518178 8.609297336383706 chr6 171115067 2004350232 11.713464320473895 11.834735202870812 chr7 159138663 1773652793 11.145329234040378 10.56096137261162 chr8 146364022 1721674347 11.762961440073026 10.318177714362237 chr9 141213431 1421733109 10.067973697204481 14.239056655839251 chr10 135534747 1607268935 11.858722361432527 18.226635736378952 chr11 135006516 1675023236 12.406980682324992 11.26471212275415 chr12 133851895 1654770812 12.362699922926007 10.241745850984989 chr13 115169878 1018725548 8.845416576719826 8.738111361820811 chr14 107349540 1076671405 10.029585641447555 9.980071637360409 chr15 102531392 1080895644 10.5420946981779 10.228614959136927 chr16 90354753 1063200337 11.766955270189273 15.066757046139717 chr17 81195210 1057740286 13.02712667409814 17.879169502237556 chr18 78077248 892543494 11.431543975525367 24.973991743406135 chr19 59128983 759536314 12.845414811210265 18.193784409298765 chr20 63025520 815354171 12.936889231536686 11.769788589560147 chr21 48129895 423255275 8.794020327698616 21.409541288040515 chr22 51304566 458714127 8.941000046662513 11.039607522556212 chrMT 16571 33054026 1994.6910868384527 609.7502070277427 chrX 155270560 1052459750 6.77823117273487 6.6050086580835545 chrY 59373566 200254006 3.372780506395725 18.66256457705038