BamQC report ----------------------------------- >>>>>>> Input bam file = SRR617488.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 32,000,000 number of mapped reads = 30,438,445 (95.12%) number of supplementary alignments = 151,318 (0.47%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 15,357,574 number of mapped paired reads (second in pair) = 15,080,871 number of mapped paired reads (both in pair) = 29,881,072 number of mapped paired reads (singletons) = 557,373 number of mapped bases = 2,964,384,368 bp number of sequenced bases = 2,962,631,581 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 6,225,214 duplication rate = 9.89% >>>>>>> Insert size mean insert size = 34,647.7144 std insert size = 1,734,874.5532 median insert size = 219 >>>>>>> Mapping quality mean mapping quality = 52.7381 >>>>>>> ACTG content number of A's = 873,315,419 bp (29.48%) number of C's = 598,535,386 bp (20.2%) number of T's = 873,239,640 bp (29.48%) number of G's = 614,131,903 bp (20.73%) number of N's = 3,409,233 bp (0.12%) GC percentage = 40.93% >>>>>>> Mismatches and indels general error rate = 0.0135 number of mismatches = 38,979,750 number of insertions = 440,911 mapped reads with insertion percentage = 1.42% number of deletions = 1,030,481 mapped reads with deletion percentage = 3.32% homopolymer indels = 47.36% >>>>>>> Coverage mean coverageData = 0.9576X std coverageData = 9.5896X There is a 38.18% of reference with a coverageData >= 1X There is a 20.59% of reference with a coverageData >= 2X There is a 11.61% of reference with a coverageData >= 3X There is a 6.9% of reference with a coverageData >= 4X There is a 4.25% of reference with a coverageData >= 5X There is a 2.73% of reference with a coverageData >= 6X There is a 1.8% of reference with a coverageData >= 7X There is a 1.23% of reference with a coverageData >= 8X There is a 0.87% of reference with a coverageData >= 9X There is a 0.63% of reference with a coverageData >= 10X There is a 0.46% of reference with a coverageData >= 11X There is a 0.35% of reference with a coverageData >= 12X There is a 0.27% of reference with a coverageData >= 13X There is a 0.21% of reference with a coverageData >= 14X There is a 0.17% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.08% of reference with a coverageData >= 19X There is a 0.07% of reference with a coverageData >= 20X There is a 0.06% of reference with a coverageData >= 21X There is a 0.06% of reference with a coverageData >= 22X There is a 0.05% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.04% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.03% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% of reference with a coverageData >= 37X There is a 0.02% of reference with a coverageData >= 38X There is a 0.02% of reference with a coverageData >= 39X There is a 0.02% of reference with a coverageData >= 40X There is a 0.02% of reference with a coverageData >= 41X There is a 0.02% of reference with a coverageData >= 42X There is a 0.02% of reference with a coverageData >= 43X There is a 0.02% of reference with a coverageData >= 44X There is a 0.02% of reference with a coverageData >= 45X There is a 0.02% of reference with a coverageData >= 46X There is a 0.02% of reference with a coverageData >= 47X There is a 0.01% of reference with a coverageData >= 48X There is a 0.01% of reference with a coverageData >= 49X There is a 0.01% of reference with a coverageData >= 50X There is a 0.01% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 191049923 0.7664972798603379 9.454082238560824 chr2 243199373 306212060 1.259098887561688 11.267324422557182 chr3 198022430 245082130 1.2376483310501745 2.241465241491365 chr4 191154276 153136380 0.8011140697684419 5.985233105877483 chr5 180915260 190239604 1.0515398424654725 2.06973780745679 chr6 171115067 139873778 0.8174252592262959 5.404263954863142 chr7 159138663 228593366 1.4364414133603725 13.157675300846774 chr8 146364022 131832338 0.9007154640776406 3.8374992680810966 chr9 141213431 122355799 0.8664600678104054 17.888319537746423 chr10 135534747 125347952 0.9248399747999677 18.47561533784902 chr11 135006516 167196832 1.2384352767091626 12.545292706508096 chr12 133851895 129384478 0.9666241781634843 1.9835076495562165 chr13 115169878 125700485 1.0914354272390563 2.1198482332318016 chr14 107349540 86159162 0.8026039235938971 2.1903722174803097 chr15 102531392 66903163 0.6525139442172013 1.4718448268721043 chr16 90354753 80098627 0.8864904649786381 14.801240153035701 chr17 81195210 82476856 1.0157847488786593 13.296776756502485 chr18 78077248 53200449 0.6813822254595858 16.96120711195173 chr19 59128983 35383431 0.5984109518677161 5.729130998170789 chr20 63025520 87711961 1.391689604464985 2.7945855364290813 chr21 48129895 42798297 0.8892248154707173 3.757588224818892 chr22 51304566 22242217 0.43353289451858923 1.2395849691553493 chrMT 16571 2102559 126.88184177176996 91.60882817526394 chrX 155270560 139135706 0.8960855554330454 4.078577745030128 chrY 59373566 10166815 0.17123470400952504 13.450422690506045