BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472671.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 = 19,160,876 number of mapped reads = 18,997,142 (99.15%) number of supplementary alignments = 114,181 (0.6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 9,523,793 number of mapped paired reads (second in pair) = 9,473,349 number of mapped paired reads (both in pair) = 18,895,702 number of mapped paired reads (singletons) = 101,440 number of mapped bases = 1,867,911,088 bp number of sequenced bases = 1,867,654,088 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 13,572,582 duplication rate = 49.56% >>>>>>> Insert size mean insert size = 22,283.3876 std insert size = 1,520,645.1492 median insert size = 213 >>>>>>> Mapping quality mean mapping quality = 54.7971 >>>>>>> ACTG content number of A's = 496,460,555 bp (26.58%) number of C's = 439,600,966 bp (23.54%) number of T's = 497,717,471 bp (26.65%) number of G's = 433,518,155 bp (23.21%) number of N's = 356,941 bp (0.02%) GC percentage = 46.75% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 11,429,418 number of insertions = 125,292 mapped reads with insertion percentage = 0.65% number of deletions = 113,275 mapped reads with deletion percentage = 0.59% homopolymer indels = 48.52% >>>>>>> Coverage mean coverageData = 0.6034X std coverageData = 28.4965X There is a 3.63% of reference with a coverageData >= 1X There is a 1.69% of reference with a coverageData >= 2X There is a 0.81% of reference with a coverageData >= 3X There is a 0.61% of reference with a coverageData >= 4X There is a 0.46% of reference with a coverageData >= 5X There is a 0.41% of reference with a coverageData >= 6X There is a 0.37% of reference with a coverageData >= 7X There is a 0.35% of reference with a coverageData >= 8X There is a 0.33% of reference with a coverageData >= 9X There is a 0.32% of reference with a coverageData >= 10X There is a 0.3% of reference with a coverageData >= 11X There is a 0.29% of reference with a coverageData >= 12X There is a 0.28% of reference with a coverageData >= 13X There is a 0.28% of reference with a coverageData >= 14X There is a 0.27% of reference with a coverageData >= 15X There is a 0.26% of reference with a coverageData >= 16X There is a 0.25% of reference with a coverageData >= 17X There is a 0.25% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.24% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.23% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.22% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.21% of reference with a coverageData >= 26X There is a 0.21% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.2% of reference with a coverageData >= 29X There is a 0.2% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.19% of reference with a coverageData >= 32X There is a 0.19% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.18% of reference with a coverageData >= 35X There is a 0.18% of reference with a coverageData >= 36X There is a 0.18% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.17% of reference with a coverageData >= 39X There is a 0.17% of reference with a coverageData >= 40X There is a 0.17% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.16% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.16% of reference with a coverageData >= 45X There is a 0.16% of reference with a coverageData >= 46X There is a 0.16% of reference with a coverageData >= 47X There is a 0.15% of reference with a coverageData >= 48X There is a 0.15% of reference with a coverageData >= 49X There is a 0.15% of reference with a coverageData >= 50X There is a 0.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 229902568 0.9223751061386523 35.76266334178915 chr2 243199373 150400462 0.618424546678416 34.510219923076704 chr3 198022430 178435547 0.9010875535665328 28.079481147811585 chr4 191154276 46601261 0.24378874475190918 13.094744313192772 chr5 180915260 53488852 0.2956569390553345 11.695939493354366 chr6 171115067 158055258 0.9236782053797752 39.5146121718362 chr7 159138663 159934764 1.005002561822453 46.243843469799444 chr8 146364022 73792656 0.5041720977030817 16.85809284229543 chr9 141213431 108637174 0.7693119077320627 23.68119814464192 chr10 135534747 60081506 0.44329227249747255 34.8411020553664 chr11 135006516 35734784 0.26468932803213735 10.104683815003465 chr12 133851895 59801642 0.4467747132007358 16.829531860419497 chr13 115169878 37943337 0.32945538936839025 15.828853818756368 chr14 107349540 32967710 0.3071062065100605 18.507384152326416 chr15 102531392 13356077 0.1302632953622633 5.297618631367292 chr16 90354753 109466520 1.211519221351864 44.39373137985376 chr17 81195210 49874009 0.6142481680877481 18.81275141869569 chr18 78077248 12990572 0.16638101793751747 8.94215613204835 chr19 59128983 67214737 1.136747726575984 59.673589672620906 chr20 63025520 86592005 1.3739197233120806 41.49816760161556 chr21 48129895 9595790 0.19937275990317452 12.094833511072446 chr22 51304566 28217991 0.5500093500449843 23.359171799944573 chrMT 16571 11195 0.6755778166676725 1.1059008249854607 chrX 155270560 102853149 0.6624124302765444 26.712847867229254 chrY 59373566 1961522 0.033036957894696774 2.7770465154092983