BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124857.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 144,422,752 number of mapped reads = 140,396,049 (97.21%) number of supplementary alignments = 2,170,986 (1.5%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 70,918,005 number of mapped paired reads (second in pair) = 69,478,044 number of mapped paired reads (both in pair) = 138,350,604 number of mapped paired reads (singletons) = 2,045,445 number of mapped bases = 19,198,943,585 bp number of sequenced bases = 19,183,294,957 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,336,203 duplication rate = 28.45% >>>>>>> Insert size mean insert size = 59,290.9482 std insert size = 2,315,212.782 median insert size = 260 >>>>>>> Mapping quality mean mapping quality = 53.7654 >>>>>>> ACTG content number of A's = 5,486,060,247 bp (28.6%) number of C's = 3,838,074,085 bp (20.01%) number of T's = 5,598,180,912 bp (29.18%) number of G's = 4,260,935,630 bp (22.21%) number of N's = 44,083 bp (0%) GC percentage = 42.22% >>>>>>> Mismatches and indels general error rate = 0.0132 number of mismatches = 241,298,818 number of insertions = 3,938,213 mapped reads with insertion percentage = 2.55% number of deletions = 6,964,056 mapped reads with deletion percentage = 4.7% homopolymer indels = 44.26% >>>>>>> Coverage mean coverageData = 6.2018X std coverageData = 74.4631X There is a 57.93% of reference with a coverageData >= 1X There is a 49.97% of reference with a coverageData >= 2X There is a 43.34% of reference with a coverageData >= 3X There is a 38.31% of reference with a coverageData >= 4X There is a 33.94% of reference with a coverageData >= 5X There is a 30.3% of reference with a coverageData >= 6X There is a 27.13% of reference with a coverageData >= 7X There is a 24.39% of reference with a coverageData >= 8X There is a 21.99% of reference with a coverageData >= 9X There is a 19.88% of reference with a coverageData >= 10X There is a 18.02% of reference with a coverageData >= 11X There is a 16.36% of reference with a coverageData >= 12X There is a 14.89% of reference with a coverageData >= 13X There is a 13.58% of reference with a coverageData >= 14X There is a 12.4% of reference with a coverageData >= 15X There is a 11.35% of reference with a coverageData >= 16X There is a 10.4% of reference with a coverageData >= 17X There is a 9.54% of reference with a coverageData >= 18X There is a 8.76% of reference with a coverageData >= 19X There is a 8.06% of reference with a coverageData >= 20X There is a 7.43% of reference with a coverageData >= 21X There is a 6.85% of reference with a coverageData >= 22X There is a 6.32% of reference with a coverageData >= 23X There is a 5.84% of reference with a coverageData >= 24X There is a 5.41% of reference with a coverageData >= 25X There is a 5% of reference with a coverageData >= 26X There is a 4.64% of reference with a coverageData >= 27X There is a 4.3% of reference with a coverageData >= 28X There is a 4% of reference with a coverageData >= 29X There is a 3.71% of reference with a coverageData >= 30X There is a 3.45% of reference with a coverageData >= 31X There is a 3.22% of reference with a coverageData >= 32X There is a 3% of reference with a coverageData >= 33X There is a 2.79% of reference with a coverageData >= 34X There is a 2.61% of reference with a coverageData >= 35X There is a 2.43% of reference with a coverageData >= 36X There is a 2.27% of reference with a coverageData >= 37X There is a 2.13% of reference with a coverageData >= 38X There is a 1.99% of reference with a coverageData >= 39X There is a 1.86% of reference with a coverageData >= 40X There is a 1.75% of reference with a coverageData >= 41X There is a 1.64% of reference with a coverageData >= 42X There is a 1.54% of reference with a coverageData >= 43X There is a 1.44% of reference with a coverageData >= 44X There is a 1.36% of reference with a coverageData >= 45X There is a 1.27% of reference with a coverageData >= 46X There is a 1.2% of reference with a coverageData >= 47X There is a 1.13% of reference with a coverageData >= 48X There is a 1.06% of reference with a coverageData >= 49X There is a 1% of reference with a coverageData >= 50X There is a 0.94% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 1572512095 6.308959587306304 52.208587962259074 chr2 243199373 1681428894 6.913787947964816 94.81675896376144 chr3 198022430 1416047033 7.150942612915113 12.414938786697991 chr4 191154276 1035504269 5.417112767071975 102.36324979364406 chr5 180915260 937429558 5.181594731146505 11.799192406498566 chr6 171115067 1157888613 6.766725065771093 31.42522675220272 chr7 159138663 1282379128 8.058249980396027 58.5732841612 chr8 146364022 1219875190 8.334529027905505 21.32069012300163 chr9 141213431 949477165 6.723702967035763 112.1974870740571 chr10 135534747 1122373403 8.281074985147535 212.07423443576675 chr11 135006516 745185245 5.519624289837981 25.267715511341887 chr12 133851895 965927062 7.216386902852589 12.807466359947538 chr13 115169878 452760793 3.9312431415443543 8.092438439875647 chr14 107349540 464791484 4.329701682932223 13.319755500277235 chr15 102531392 474360682 4.6264921673939625 9.137782372151662 chr16 90354753 695795189 7.700703791420912 104.50379358320075 chr17 81195210 469575954 5.783296256022985 67.40380544031035 chr18 78077248 377261247 4.831897340951361 79.72728441191458 chr19 59128983 324558650 5.488994288976693 28.02973279750384 chr20 63025520 352965912 5.600364931538843 32.36392802392616 chr21 48129895 206545087 4.291409465987823 47.01007224929217 chr22 51304566 186176524 3.6288490190132396 11.48992318968191 chrMT 16571 7256964 437.93156719570334 196.62773109028055 chrX 155270560 782962201 5.042566994026427 15.481065119284505 chrY 59373566 317905243 5.354322881667576 149.02676445342786