BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084856.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 = 2,361,656 number of mapped reads = 2,089,805 (88.49%) number of supplementary alignments = 19,328 (0.82%) number of secondary alignments = 0 number of mapped bases = 142,599,319 bp number of sequenced bases = 142,547,013 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 120,176 duplication rate = 4.92% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.8696 >>>>>>> ACTG content number of A's = 40,917,571 bp (28.7%) number of C's = 25,780,213 bp (18.09%) number of T's = 46,051,727 bp (32.31%) number of G's = 29,775,384 bp (20.89%) number of N's = 22,118 bp (0.02%) GC percentage = 38.97% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,166,985 number of insertions = 11,225 mapped reads with insertion percentage = 0.53% number of deletions = 30,157 mapped reads with deletion percentage = 1.43% homopolymer indels = 48.13% >>>>>>> Coverage mean coverageData = 0.0461X std coverageData = 0.3824X There is a 3.71% of reference with a coverageData >= 1X There is a 0.68% of reference with a coverageData >= 2X There is a 0.13% of reference with a coverageData >= 3X There is a 0.03% 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 10737581 0.043079455356703 0.500267705168346 chr2 243199373 12402185 0.050995957954217255 0.36171156239143726 chr3 198022430 9855188 0.049768038903471694 0.26650875839345756 chr4 191154276 10248244 0.05361242350655028 0.28152498975828116 chr5 180915260 8999412 0.049743797178856 0.2684878695217167 chr6 171115067 8760995 0.0511994364587427 0.2755510859962733 chr7 159138663 7782445 0.04890354646249604 0.3308262310595718 chr8 146364022 7465247 0.051004658781513945 0.9838190100211449 chr9 141213431 5862862 0.04151773636885857 0.31710700132260766 chr10 135534747 6700355 0.049436437137408015 0.3380766733212145 chr11 135006516 6650925 0.049263733314916444 0.28489867900109483 chr12 133851895 6345750 0.04740874232673359 0.26248542733311137 chr13 115169878 4887630 0.04243844037066706 0.24659126782678367 chr14 107349540 4328435 0.04032094594909303 0.2515961057339147 chr15 102531392 3994042 0.0389543331275557 0.23469059476010323 chr16 90354753 3609678 0.03995006217326497 0.2534712626793521 chr17 81195210 3242633 0.03993625978675343 0.24962079875770007 chr18 78077248 3922069 0.05023318700987002 0.6418630608970736 chr19 59128983 2116690 0.03579784215128476 0.36479981001510486 chr20 63025520 2675526 0.0424514704519693 0.26089329045273363 chr21 48129895 1839459 0.03821863729393135 0.24215979626745307 chr22 51304566 1337568 0.02607112980938188 0.18972185805368144 chrMT 16571 79855 4.818960835194014 3.1083403114393624 chrX 155270560 8434394 0.0543206258803987 0.29460564171579645 chrY 59373566 320151 0.0053921470709709434 0.10612014000069288