BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237800.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,081,258 number of mapped reads = 1,746,014 (83.89%) number of supplementary alignments = 17,441 (0.84%) number of secondary alignments = 0 number of mapped bases = 116,462,705 bp number of sequenced bases = 116,410,765 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 367,058 duplication rate = 12.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4576 >>>>>>> ACTG content number of A's = 32,257,321 bp (27.71%) number of C's = 21,700,022 bp (18.64%) number of T's = 36,506,200 bp (31.36%) number of G's = 25,758,792 bp (22.13%) number of N's = 188,430 bp (0.16%) GC percentage = 40.77% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 968,850 number of insertions = 8,165 mapped reads with insertion percentage = 0.46% number of deletions = 29,063 mapped reads with deletion percentage = 1.65% homopolymer indels = 47.23% >>>>>>> Coverage mean coverageData = 0.0376X std coverageData = 0.5718X There is a 1.13% of reference with a coverageData >= 1X There is a 0.63% of reference with a coverageData >= 2X There is a 0.46% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.27% of reference with a coverageData >= 5X There is a 0.2% of reference with a coverageData >= 6X There is a 0.15% of reference with a coverageData >= 7X There is a 0.12% of reference with a coverageData >= 8X There is a 0.09% of reference with a coverageData >= 9X There is a 0.07% of reference with a coverageData >= 10X There is a 0.05% of reference with a coverageData >= 11X There is a 0.04% of reference with a coverageData >= 12X There is a 0.03% of reference with a coverageData >= 13X There is a 0.03% of reference with a coverageData >= 14X There is a 0.02% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 8799563 0.03530407653427672 0.8118017612530767 chr2 243199373 9393927 0.03862644415616976 0.5948112514055667 chr3 198022430 8822840 0.0445547506916262 0.5701601825110432 chr4 191154276 8031480 0.04201569626410031 0.5549837114615871 chr5 180915260 6932733 0.03832033295588222 0.5172148291743427 chr6 171115067 7379454 0.043125682205413275 0.5668533281133913 chr7 159138663 5888613 0.03700303175225244 0.5926115201270016 chr8 146364022 5991792 0.04093760145508983 0.5786868453463891 chr9 141213431 4990592 0.03534077434886487 0.5220673615618769 chr10 135534747 5633552 0.041565370686824685 0.610883766879495 chr11 135006516 5331465 0.03949042726204415 0.5435110502928641 chr12 133851895 5285244 0.03948576148286881 0.5397956886254015 chr13 115169878 4220819 0.03664863654713605 0.5313674371162015 chr14 107349540 3670405 0.0341911572234031 0.4922694108914659 chr15 102531392 2789938 0.027210573713853412 0.4226218932895227 chr16 90354753 2982089 0.03300422945099524 0.47700728580045204 chr17 81195210 3101852 0.038202401348552455 0.5320207017847484 chr18 78077248 3139172 0.04020597652212332 0.6474482270321317 chr19 59128983 2330852 0.039419788430996694 0.648076710799145 chr20 63025520 2253683 0.03575826109804409 0.5087581772515132 chr21 48129895 1556318 0.03233578631326746 0.47025291387491464 chr22 51304566 1128513 0.02199634629011383 0.3752646735472115 chrMT 16571 34699 2.093959326534307 3.3133112624808017 chrX 155270560 6440862 0.04148154035124237 0.5575491051226605 chrY 59373566 332248 0.00559589093907548 0.17026475279090242