BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082985.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 4,263,673 number of mapped reads = 3,660,741 (85.86%) number of supplementary alignments = 21,969 (0.52%) number of secondary alignments = 0 number of mapped bases = 244,710,848 bp number of sequenced bases = 244,613,235 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 188,611 duplication rate = 3.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1375 >>>>>>> ACTG content number of A's = 67,762,705 bp (27.7%) number of C's = 44,927,763 bp (18.37%) number of T's = 77,925,197 bp (31.86%) number of G's = 53,973,300 bp (22.06%) number of N's = 24,270 bp (0.01%) GC percentage = 40.43% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 2,184,098 number of insertions = 20,432 mapped reads with insertion percentage = 0.55% number of deletions = 56,472 mapped reads with deletion percentage = 1.53% homopolymer indels = 48.09% >>>>>>> Coverage mean coverageData = 0.079X std coverageData = 0.6283X There is a 6.15% of reference with a coverageData >= 1X There is a 1.17% of reference with a coverageData >= 2X There is a 0.28% of reference with a coverageData >= 3X There is a 0.09% 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% 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 23110401 0.09271953228152639 0.9497708122482724 chr2 243199373 25826739 0.10619574664775143 1.0021040807981532 chr3 198022430 15781000 0.07969299235445197 0.34555315835715533 chr4 191154276 12926226 0.06762195578612115 0.3355557391149881 chr5 180915260 13835882 0.07647714183977626 0.34420140408947375 chr6 171115067 17571324 0.10268718183653576 0.6552750783207819 chr7 159138663 12314066 0.0773794737737617 0.6183814514966457 chr8 146364022 19713792 0.1346901494685627 0.7625548287665559 chr9 141213431 7179871 0.050844108447446475 0.6374492768906173 chr10 135534747 9730784 0.07179549315128762 0.48847152845547614 chr11 135006516 10536081 0.07804127765210978 0.5344439569128479 chr12 133851895 7985563 0.05965969327516805 0.3151274389838927 chr13 115169878 5919939 0.051401799696271275 0.2747786760638808 chr14 107349540 5620424 0.05235629328267266 0.35896173067876835 chr15 102531392 4571363 0.044585008657641166 0.26322972050294696 chr16 90354753 9854738 0.10906717879025135 0.47093952115999016 chr17 81195210 6234244 0.07678093325948661 0.42215590343024756 chr18 78077248 9368388 0.11998870656916596 1.4875540482804657 chr19 59128983 4079804 0.06899837935653316 0.816547796693619 chr20 63025520 4713521 0.07478749877827268 0.3726290784210727 chr21 48129895 4452673 0.09251366536328409 0.3886428877016862 chr22 51304566 2985689 0.05819538557250441 0.29319395751903277 chrMT 16571 7974 0.48120210005431174 0.9162234615983826 chrX 155270560 9970108 0.06421119367380397 0.40462073067830684 chrY 59373566 420254 0.007078133053352396 0.14632104545716523