BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472518.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 = 13,966,466 number of mapped reads = 13,787,008 (98.72%) number of supplementary alignments = 60,060 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 6,919,781 number of mapped paired reads (second in pair) = 6,867,227 number of mapped paired reads (both in pair) = 13,694,928 number of mapped paired reads (singletons) = 92,080 number of mapped bases = 1,356,372,847 bp number of sequenced bases = 1,356,208,211 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 8,290,004 duplication rate = 44.93% >>>>>>> Insert size mean insert size = 35,595.9945 std insert size = 1,876,085.3253 median insert size = 244 >>>>>>> Mapping quality mean mapping quality = 54.9358 >>>>>>> ACTG content number of A's = 378,377,800 bp (27.9%) number of C's = 302,027,883 bp (22.27%) number of T's = 375,977,767 bp (27.72%) number of G's = 299,615,145 bp (22.09%) number of N's = 209,616 bp (0.02%) GC percentage = 44.36% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 8,404,763 number of insertions = 76,860 mapped reads with insertion percentage = 0.55% number of deletions = 69,600 mapped reads with deletion percentage = 0.5% homopolymer indels = 44.52% >>>>>>> Coverage mean coverageData = 0.4381X std coverageData = 15.2459X There is a 4.55% of reference with a coverageData >= 1X There is a 1.99% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.63% of reference with a coverageData >= 4X There is a 0.47% 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 0.27% of reference with a coverageData >= 14X There is a 0.26% 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 0.24% of reference with a coverageData >= 18X There is a 0.24% of reference with a coverageData >= 19X There is a 0.23% of reference with a coverageData >= 20X There is a 0.23% of reference with a coverageData >= 21X There is a 0.22% of reference with a coverageData >= 22X There is a 0.22% of reference with a coverageData >= 23X There is a 0.21% of reference with a coverageData >= 24X There is a 0.21% of reference with a coverageData >= 25X There is a 0.2% of reference with a coverageData >= 26X There is a 0.2% of reference with a coverageData >= 27X There is a 0.2% of reference with a coverageData >= 28X There is a 0.19% of reference with a coverageData >= 29X There is a 0.19% of reference with a coverageData >= 30X There is a 0.19% of reference with a coverageData >= 31X There is a 0.18% of reference with a coverageData >= 32X There is a 0.18% of reference with a coverageData >= 33X There is a 0.18% of reference with a coverageData >= 34X There is a 0.17% of reference with a coverageData >= 35X There is a 0.17% of reference with a coverageData >= 36X There is a 0.17% of reference with a coverageData >= 37X There is a 0.17% of reference with a coverageData >= 38X There is a 0.16% of reference with a coverageData >= 39X There is a 0.16% of reference with a coverageData >= 40X There is a 0.16% of reference with a coverageData >= 41X There is a 0.16% of reference with a coverageData >= 42X There is a 0.15% of reference with a coverageData >= 43X There is a 0.15% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.15% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.14% of reference with a coverageData >= 49X There is a 0.14% of reference with a coverageData >= 50X There is a 0.14% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 176155680 0.7067411880189458 28.377780996989564 chr2 243199373 86289486 0.3548096565199615 12.283887621005213 chr3 198022430 131743085 0.6652937498039995 15.264925003715716 chr4 191154276 50158611 0.2623985821797677 11.263509665110979 chr5 180915260 77133442 0.42635122100811174 15.796134732915213 chr6 171115067 98462519 0.5754170028756147 18.058948083916007 chr7 159138663 56526394 0.3552021421720754 10.702069810589887 chr8 146364022 60942542 0.41637651908745715 11.850731876061356 chr9 141213431 67610148 0.4787798690338457 12.183888047643363 chr10 135534747 31666085 0.2336381311871265 8.37365597780784 chr11 135006516 69377891 0.5138855001635625 17.511264371575823 chr12 133851895 67423197 0.5037149231245475 15.304788742043332 chr13 115169878 34687013 0.30118129499103924 10.458534433747763 chr14 107349540 34683198 0.3230866010231623 11.67167860932536 chr15 102531392 31689206 0.30906832904404535 9.424728110162613 chr16 90354753 54682595 0.6051988764774776 18.424757831711986 chr17 81195210 43453068 0.5351678750507574 15.029669639106297 chr18 78077248 21517597 0.2755936915194552 8.955444709357174 chr19 59128983 30720668 0.5195534650071691 18.368407587813703 chr20 63025520 20129384 0.3193846556125201 7.847775638721302 chr21 48129895 9280736 0.19282684909244036 9.210136732268278 chr22 51304566 17616738 0.34337563639072594 10.463557073117897 chrMT 16571 1843 0.11121839357914429 0.3932972093901181 chrX 155270560 82800214 0.5332640907587375 16.742563699020376 chrY 59373566 1621507 0.027310251164634442 0.9782528646700565