BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708560.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 = 4,062,949 number of mapped reads = 3,334,434 (82.07%) number of supplementary alignments = 114 (0%) number of secondary alignments = 0 number of mapped bases = 166,274,676 bp number of sequenced bases = 166,259,334 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 15,321 duplication rate = 0.46% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.4308 >>>>>>> ACTG content number of A's = 51,546,449 bp (31%) number of C's = 31,511,327 bp (18.95%) number of T's = 51,366,203 bp (30.9%) number of G's = 31,828,632 bp (19.14%) number of N's = 6,723 bp (0%) GC percentage = 38.1% >>>>>>> Mismatches and indels general error rate = 0.0017 number of mismatches = 263,670 number of insertions = 11,468 mapped reads with insertion percentage = 0.34% number of deletions = 9,049 mapped reads with deletion percentage = 0.27% homopolymer indels = 47.41% >>>>>>> Coverage mean coverageData = 0.0537X std coverageData = 0.2385X There is a 5.09% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 13254024 0.053175490383231584 0.23846193258172352 chr2 243199373 14056728 0.05779919506618136 0.24645408215172687 chr3 198022430 13048383 0.06589345964495032 0.2630666342022695 chr4 191154276 13405773 0.07013064672432438 0.27162704866670234 chr5 180915260 11744706 0.06491827168144909 0.2611920508122795 chr6 171115067 10364193 0.06056855881662367 0.2526536164631671 chr7 159138663 8816066 0.0553986431317448 0.24196246585393302 chr8 146364022 9722352 0.06642583243578808 0.2642121421458354 chr9 141213431 7193834 0.05094298714404864 0.2329065192814058 chr10 135534747 7300537 0.05386468903062917 0.23785364852091365 chr11 135006516 7203214 0.05335456549371291 0.2381098495725708 chr12 133851895 7463946 0.055762721924855825 0.2425930854967778 chr13 115169878 6241555 0.0541943354320476 0.23951952243393493 chr14 107349540 5291704 0.049294146952096864 0.22850234354896032 chr15 102531392 4604429 0.04490750501075807 0.21818620617032305 chr16 90354753 2873240 0.03179954462384508 0.18297204804952363 chr17 81195210 2645742 0.032584951747769354 0.18526986889504873 chr18 78077248 4600346 0.05892044248280882 0.24870693958949075 chr19 59128983 1301911 0.02201815309422792 0.1518271372790121 chr20 63025520 2577771 0.04090043207894199 0.20729378699873377 chr21 48129895 2071011 0.04302961807832741 0.21482412401350678 chr22 51304566 807069 0.015730939035718577 0.1283180537719712 chrMT 16571 100 0.006034638826866212 0.07744818888195831 chrX 155270560 9464081 0.06095219209617071 0.2535826255957248 chrY 59373566 221961 0.0037383808141151567 0.0634489997457481