BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708630.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,407,315 number of mapped reads = 2,478,506 (72.74%) number of supplementary alignments = 803 (0.02%) number of secondary alignments = 0 number of mapped bases = 120,704,987 bp number of sequenced bases = 120,682,972 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 89,634 duplication rate = 2.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.6371 >>>>>>> ACTG content number of A's = 35,618,782 bp (29.51%) number of C's = 22,753,715 bp (18.85%) number of T's = 37,991,022 bp (31.48%) number of G's = 24,308,775 bp (20.14%) number of N's = 10,678 bp (0.01%) GC percentage = 39% >>>>>>> Mismatches and indels general error rate = 0.0064 number of mismatches = 769,465 number of insertions = 5,452 mapped reads with insertion percentage = 0.22% number of deletions = 14,642 mapped reads with deletion percentage = 0.59% homopolymer indels = 48.19% >>>>>>> Coverage mean coverageData = 0.039X std coverageData = 0.4019X There is a 3.36% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% 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 9549082 0.03831116633406502 0.73274460254667 chr2 243199373 10427664 0.04287701843705 0.40829043015057986 chr3 198022430 8400912 0.04242404256931904 0.2346846663640522 chr4 191154276 8156715 0.04267084770837143 0.23714737923686094 chr5 180915260 7641951 0.04224049977873619 0.23840786066816394 chr6 171115067 7258339 0.04241788363382402 0.29914566481326416 chr7 159138663 6844491 0.04300960477467377 0.6135830941194919 chr8 146364022 6342660 0.043334829921522655 0.6863444532603982 chr9 141213431 5028059 0.035606096136846926 0.32229615056599137 chr10 135534747 5530850 0.040807616662316124 0.30171615769611887 chr11 135006516 5404718 0.04003301588791462 0.3364855145432978 chr12 133851895 5409396 0.04041329411137586 0.2375528208232032 chr13 115169878 4095643 0.03556175513184098 0.21458558878654677 chr14 107349540 3694139 0.03441224806366194 0.22882804477488952 chr15 102531392 3417246 0.033328777980503765 0.20634476353124226 chr16 90354753 3104703 0.03436125822844095 0.22723960202615495 chr17 81195210 2876533 0.035427373117207284 0.2625423592648208 chr18 78077248 3417282 0.043767961698650035 0.6857923835568601 chr19 59128983 2011291 0.034015315298083174 0.5572677999208998 chr20 63025520 2390943 0.03793610905550641 0.22786113422740592 chr21 48129895 1568163 0.032581891151019546 0.22513940153124537 chr22 51304566 1176772 0.022936983815436622 0.16952557618168437 chrMT 16571 2623 0.15828857642870076 0.4305491638187214 chrX 155270560 6676820 0.043001197393762215 0.2684788033226855 chrY 59373566 277992 0.004682083606027639 0.09678665745579126