BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472703.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 = 1,607,938 number of mapped reads = 1,358,388 (84.48%) number of supplementary alignments = 7,136 (0.44%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 704,761 number of mapped paired reads (second in pair) = 653,627 number of mapped paired reads (both in pair) = 1,289,584 number of mapped paired reads (singletons) = 68,804 number of mapped bases = 131,742,604 bp number of sequenced bases = 131,720,371 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 416,169 duplication rate = 27.98% >>>>>>> Insert size mean insert size = 61,581.3559 std insert size = 2,483,504.702 median insert size = 291 >>>>>>> Mapping quality mean mapping quality = 54.0492 >>>>>>> ACTG content number of A's = 38,087,394 bp (28.92%) number of C's = 27,839,107 bp (21.14%) number of T's = 36,213,355 bp (27.49%) number of G's = 29,557,471 bp (22.44%) number of N's = 23,044 bp (0.02%) GC percentage = 43.57% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 1,392,411 number of insertions = 10,256 mapped reads with insertion percentage = 0.74% number of deletions = 8,963 mapped reads with deletion percentage = 0.65% homopolymer indels = 45.34% >>>>>>> Coverage mean coverageData = 0.0426X std coverageData = 1.1078X There is a 0.83% of reference with a coverageData >= 1X There is a 0.45% of reference with a coverageData >= 2X There is a 0.3% of reference with a coverageData >= 3X There is a 0.24% of reference with a coverageData >= 4X There is a 0.2% of reference with a coverageData >= 5X There is a 0.17% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.13% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.11% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.09% of reference with a coverageData >= 12X There is a 0.08% of reference with a coverageData >= 13X There is a 0.07% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.06% of reference with a coverageData >= 17X There is a 0.05% of reference with a coverageData >= 18X There is a 0.05% of reference with a coverageData >= 19X There is a 0.05% of reference with a coverageData >= 20X There is a 0.04% of reference with a coverageData >= 21X There is a 0.04% of reference with a coverageData >= 22X There is a 0.04% of reference with a coverageData >= 23X There is a 0.03% of reference with a coverageData >= 24X There is a 0.03% of reference with a coverageData >= 25X There is a 0.03% of reference with a coverageData >= 26X There is a 0.03% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.02% of reference with a coverageData >= 30X There is a 0.02% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% of reference with a coverageData >= 44X There is a 0.01% of reference with a coverageData >= 45X There is a 0.01% of reference with a coverageData >= 46X There is a 0.01% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 12596292 0.050536652424228064 1.3621129598751132 chr2 243199373 8066880 0.03316982235805353 0.9011456003849417 chr3 198022430 15749372 0.0795332730741664 1.3304516999152578 chr4 191154276 4563276 0.023872215131614423 0.6931668807701555 chr5 180915260 6834293 0.03777621080720333 0.9770892768072827 chr6 171115067 7654238 0.04473152559967148 0.9404197248314127 chr7 159138663 5054918 0.03176423569676465 0.7671048941415424 chr8 146364022 6283512 0.04293071421609335 1.2237168589499077 chr9 141213431 9057526 0.06414068361528585 1.4052052669720645 chr10 135534747 3028166 0.022342359188526024 0.6288012864113025 chr11 135006516 6309634 0.04673577384961182 1.2243791190859554 chr12 133851895 7741163 0.05783379458318465 1.4283534175282977 chr13 115169878 2923249 0.025382062139546593 0.9136230164631888 chr14 107349540 3059824 0.02850337318632199 0.7134473493747722 chr15 102531392 3364814 0.032817402888668475 1.1446152932241573 chr16 90354753 5012621 0.05547711474569578 1.2120991167786426 chr17 81195210 5118650 0.06304128039080138 1.1789075809038942 chr18 78077248 2489700 0.031887650548338996 0.9728290297986294 chr19 59128983 3215331 0.054378256429676794 1.616877127702924 chr20 63025520 2315374 0.036737086818165086 0.8002189774952195 chr21 48129895 473834 0.009844899931736813 0.49433342693624344 chr22 51304566 1170314 0.02281110807954208 0.6364151900742189 chrMT 16571 6808 0.4108382113330517 1.1107033931128356 chrX 155270560 9508259 0.06123671480285767 1.6411224493261887 chrY 59373566 144556 0.002434686169936298 0.12606237100232184