BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013261.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 = 1,951,991 number of mapped reads = 1,729,536 (88.6%) number of supplementary alignments = 9,299 (0.48%) number of secondary alignments = 0 number of mapped bases = 117,037,010 bp number of sequenced bases = 116,985,341 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 94,917 duplication rate = 3.79% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.5435 >>>>>>> ACTG content number of A's = 33,091,668 bp (28.29%) number of C's = 21,198,208 bp (18.12%) number of T's = 37,780,456 bp (32.3%) number of G's = 24,889,160 bp (21.28%) number of N's = 25,849 bp (0.02%) GC percentage = 39.4% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 966,097 number of insertions = 8,651 mapped reads with insertion percentage = 0.5% number of deletions = 30,506 mapped reads with deletion percentage = 1.74% homopolymer indels = 46.19% >>>>>>> Coverage mean coverageData = 0.0378X std coverageData = 0.6073X There is a 3.11% of reference with a coverageData >= 1X There is a 0.47% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.02% 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 8701638 0.03491119887721363 0.6087404327111047 chr2 243199373 13712639 0.05638435178038062 0.5374759042498745 chr3 198022430 9948612 0.05023982384217788 0.25975664706577367 chr4 191154276 7926049 0.0414641470013467 0.2461159372214496 chr5 180915260 6500082 0.03592887631480064 0.21902139345964247 chr6 171115067 11455772 0.06694776912894526 0.399967279548158 chr7 159138663 8361380 0.052541474474999204 2.1545355946895235 chr8 146364022 4953124 0.033841130711753736 0.46426579749711 chr9 141213431 3611471 0.02557455742294088 0.29214734666698444 chr10 135534747 2233390 0.01647835739125997 0.4931515872487052 chr11 135006516 5846273 0.04330363580377113 0.27975708179279235 chr12 133851895 4553822 0.03402134874519334 0.22226894119739868 chr13 115169878 3929890 0.034122550689860066 0.21569038401734072 chr14 107349540 3833969 0.03571481535924607 0.23407859204037096 chr15 102531392 990836 0.009663733035049402 0.11494183346955017 chr16 90354753 3176518 0.03515606976425468 0.24253032448434161 chr17 81195210 2366428 0.029144921233654055 0.20661603334820403 chr18 78077248 3604196 0.04616192414978561 0.5692022353431816 chr19 59128983 1072743 0.018142422642378274 0.6149587719485136 chr20 63025520 2392780 0.03796525597884794 0.23893967818655343 chr21 48129895 1781006 0.03700415303212276 0.22967496627316417 chr22 51304566 1372001 0.02674227865020825 0.18747237678647288 chrMT 16571 27388 1.6527668819021182 1.6989149447177283 chrX 155270560 4505629 0.02901792200659288 0.22111606726344668 chrY 59373566 179374 0.0030211087540202657 0.08394344202267787