BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004109.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 = 4,863,485 number of mapped reads = 4,367,531 (89.8%) number of supplementary alignments = 31,274 (0.64%) number of secondary alignments = 0 number of mapped bases = 296,014,217 bp number of sequenced bases = 295,891,460 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 216,506 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.2985 >>>>>>> ACTG content number of A's = 80,927,930 bp (27.35%) number of C's = 59,447,788 bp (20.09%) number of T's = 88,703,769 bp (29.98%) number of G's = 66,772,805 bp (22.57%) number of N's = 39,168 bp (0.01%) GC percentage = 42.66% >>>>>>> Mismatches and indels general error rate = 0.01 number of mismatches = 2,914,632 number of insertions = 27,016 mapped reads with insertion percentage = 0.61% number of deletions = 72,655 mapped reads with deletion percentage = 1.64% homopolymer indels = 44.56% >>>>>>> Coverage mean coverageData = 0.0956X std coverageData = 1.0212X There is a 7.62% of reference with a coverageData >= 1X There is a 1.25% of reference with a coverageData >= 2X There is a 0.27% of reference with a coverageData >= 3X There is a 0.08% of reference with a coverageData >= 4X There is a 0.03% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 20383955 0.08178095973530192 2.184713351292947 chr2 243199373 28341207 0.11653486869803731 1.1915836958284525 chr3 198022430 21962905 0.11091119829203187 0.4208963699740343 chr4 191154276 15556100 0.0813798170018441 0.4532833597771455 chr5 180915260 17850294 0.0986666022534528 0.38185546659569103 chr6 171115067 16183725 0.09457802450558021 0.673308121031539 chr7 159138663 17812858 0.1119329373780148 1.718712616981238 chr8 146364022 14698419 0.1004237161506808 0.9327553667819743 chr9 141213431 10783448 0.07636276467215077 0.8554753303497914 chr10 135534747 12779938 0.0942927056188772 1.0503607436154836 chr11 135006516 14014943 0.10380938205975185 0.8156080915070992 chr12 133851895 15975559 0.11935250524469601 0.4301658784635781 chr13 115169878 8179752 0.07102336254971113 0.31120441686286193 chr14 107349540 7057240 0.06574075678386698 0.4238576180498336 chr15 102531392 8746341 0.08530403059386925 0.3659283303834952 chr16 90354753 10216252 0.11306823006864951 0.5775744267072004 chr17 81195210 7932246 0.09769352157596489 0.5391697606732961 chr18 78077248 7905303 0.10124976484826924 1.834887098893406 chr19 59128983 7361127 0.12449270436462606 1.3686570146404493 chr20 63025520 6065993 0.09624661565664194 0.4467595293416451 chr21 48129895 3720421 0.07729958687838401 0.4403296242465091 chr22 51304566 3065558 0.05975214759637573 0.29208333167859934 chrMT 16571 141738 8.553376380423632 6.247019630680495 chrX 155270560 18374995 0.11834178352934388 0.5247843619644589 chrY 59373566 903900 0.01522394662971734 0.3331299115542759