BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472570.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 = 242,144,252 number of mapped reads = 238,375,939 (98.44%) number of supplementary alignments = 217,862 (0.09%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 119,684,233 number of mapped paired reads (second in pair) = 118,691,706 number of mapped paired reads (both in pair) = 236,961,460 number of mapped paired reads (singletons) = 1,414,479 number of mapped bases = 22,944,209,522 bp number of sequenced bases = 22,939,651,324 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 146,411,492 duplication rate = 49.97% >>>>>>> Insert size mean insert size = 9,864.1846 std insert size = 931,228.8711 median insert size = 190 >>>>>>> Mapping quality mean mapping quality = 51.941 >>>>>>> ACTG content number of A's = 5,919,168,150 bp (25.8%) number of C's = 5,548,303,102 bp (24.19%) number of T's = 5,971,673,805 bp (26.03%) number of G's = 5,495,914,445 bp (23.96%) number of N's = 4,591,822 bp (0.02%) GC percentage = 48.14% >>>>>>> Mismatches and indels general error rate = 0.0104 number of mismatches = 233,722,140 number of insertions = 1,753,971 mapped reads with insertion percentage = 0.71% number of deletions = 1,959,979 mapped reads with deletion percentage = 0.8% homopolymer indels = 40.63% >>>>>>> Coverage mean coverageData = 7.4117X std coverageData = 64.062X There is a 70.32% of reference with a coverageData >= 1X There is a 56.77% of reference with a coverageData >= 2X There is a 43.86% of reference with a coverageData >= 3X There is a 34.88% of reference with a coverageData >= 4X There is a 27.09% of reference with a coverageData >= 5X There is a 21.83% of reference with a coverageData >= 6X There is a 17.4% of reference with a coverageData >= 7X There is a 14.38% of reference with a coverageData >= 8X There is a 11.87% of reference with a coverageData >= 9X There is a 10.13% of reference with a coverageData >= 10X There is a 8.71% of reference with a coverageData >= 11X There is a 7.69% of reference with a coverageData >= 12X There is a 6.87% of reference with a coverageData >= 13X There is a 6.27% of reference with a coverageData >= 14X There is a 5.78% of reference with a coverageData >= 15X There is a 5.41% of reference with a coverageData >= 16X There is a 5.11% of reference with a coverageData >= 17X There is a 4.86% of reference with a coverageData >= 18X There is a 4.66% of reference with a coverageData >= 19X There is a 4.49% of reference with a coverageData >= 20X There is a 4.34% of reference with a coverageData >= 21X There is a 4.21% of reference with a coverageData >= 22X There is a 4.1% of reference with a coverageData >= 23X There is a 3.99% of reference with a coverageData >= 24X There is a 3.9% of reference with a coverageData >= 25X There is a 3.81% of reference with a coverageData >= 26X There is a 3.73% of reference with a coverageData >= 27X There is a 3.66% of reference with a coverageData >= 28X There is a 3.59% of reference with a coverageData >= 29X There is a 3.52% of reference with a coverageData >= 30X There is a 3.46% of reference with a coverageData >= 31X There is a 3.4% of reference with a coverageData >= 32X There is a 3.34% of reference with a coverageData >= 33X There is a 3.28% of reference with a coverageData >= 34X There is a 3.23% of reference with a coverageData >= 35X There is a 3.18% of reference with a coverageData >= 36X There is a 3.13% of reference with a coverageData >= 37X There is a 3.08% of reference with a coverageData >= 38X There is a 3.04% of reference with a coverageData >= 39X There is a 2.99% of reference with a coverageData >= 40X There is a 2.95% of reference with a coverageData >= 41X There is a 2.9% of reference with a coverageData >= 42X There is a 2.86% of reference with a coverageData >= 43X There is a 2.82% of reference with a coverageData >= 44X There is a 2.78% of reference with a coverageData >= 45X There is a 2.74% of reference with a coverageData >= 46X There is a 2.71% of reference with a coverageData >= 47X There is a 2.67% of reference with a coverageData >= 48X There is a 2.63% of reference with a coverageData >= 49X There is a 2.6% of reference with a coverageData >= 50X There is a 2.56% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2174179293 8.722864096695671 65.60088144749106 chr2 243199373 1653882001 6.800519181437199 51.52836707195293 chr3 198022430 1247096205 6.297752254630953 31.639879747824136 chr4 191154276 1059960935 5.545054796472353 41.278793927316954 chr5 180915260 1174223871 6.49046338600735 45.48716554082652 chr6 171115067 1120425878 6.547792065557851 30.884436243738875 chr7 159138663 1501295138 9.433880552333155 180.60984110261856 chr8 146364022 1217647878 8.319311408373295 116.21904988407053 chr9 141213431 999532863 7.0781713603431955 36.98189896668877 chr10 135534747 1004549210 7.4117466718700555 52.51696335453945 chr11 135006516 1123712957 8.323397938807634 35.070773666596786 chr12 133851895 1001852202 7.484781608807257 28.24067742231527 chr13 115169878 527035831 4.57616036547334 20.025934238722215 chr14 107349540 617409978 5.751398450333369 25.514197943378722 chr15 102531392 921174963 8.984321240854703 45.88095613155465 chr16 90354753 953766646 10.555799383348432 52.162418147964466 chr17 81195210 1041484299 12.826917979521205 66.14791292094577 chr18 78077248 440543955 5.642411410299707 41.601435575258975 chr19 59128983 1030685661 17.431141357530198 68.44435587946556 chr20 63025520 537826634 8.533473964197361 36.430019943193344 chr21 48129895 307454718 6.388019712072922 45.3248992439439 chr22 51304566 494736391 9.643125935418691 50.14336422859093 chrMT 16571 5920402 357.27487779856375 88.03112693043033 chrX 155270560 585040092 3.767875197977002 17.32344282040288 chrY 59373566 202771521 3.4151817830850852 57.24117143372408