BamQC report ----------------------------------- >>>>>>> Input bam file = SRR21672004.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP398595/SRP398595.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 = 220,558,222 number of mapped reads = 219,223,887 (99.4%) number of supplementary alignments = 884,235 (0.4%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 109,624,014 number of mapped paired reads (second in pair) = 109,599,873 number of mapped paired reads (both in pair) = 218,833,598 number of mapped paired reads (singletons) = 390,289 number of mapped bases = 32,512,093,908 bp number of sequenced bases = 32,499,005,549 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 60,727,368 duplication rate = 25.11% >>>>>>> Insert size mean insert size = 37,968.7501 std insert size = 1,850,289.3024 median insert size = 369 >>>>>>> Mapping quality mean mapping quality = 54.5693 >>>>>>> ACTG content number of A's = 9,485,796,163 bp (29.19%) number of C's = 6,777,898,887 bp (20.86%) number of T's = 9,437,843,193 bp (29.04%) number of G's = 6,797,325,303 bp (20.92%) number of N's = 142,003 bp (0%) GC percentage = 41.77% >>>>>>> Mismatches and indels general error rate = 0.0063 number of mismatches = 192,067,164 number of insertions = 4,476,362 mapped reads with insertion percentage = 1.93% number of deletions = 4,742,950 mapped reads with deletion percentage = 2.08% homopolymer indels = 45.95% >>>>>>> Coverage mean coverageData = 10.5024X std coverageData = 105.7071X There is a 92.12% of reference with a coverageData >= 1X There is a 91.55% of reference with a coverageData >= 2X There is a 90.41% of reference with a coverageData >= 3X There is a 88.43% of reference with a coverageData >= 4X There is a 85.4% of reference with a coverageData >= 5X There is a 81.15% of reference with a coverageData >= 6X There is a 75.66% of reference with a coverageData >= 7X There is a 69.03% of reference with a coverageData >= 8X There is a 61.54% of reference with a coverageData >= 9X There is a 53.55% of reference with a coverageData >= 10X There is a 45.47% of reference with a coverageData >= 11X There is a 37.69% of reference with a coverageData >= 12X There is a 30.52% of reference with a coverageData >= 13X There is a 24.17% of reference with a coverageData >= 14X There is a 18.75% of reference with a coverageData >= 15X There is a 14.26% of reference with a coverageData >= 16X There is a 10.67% of reference with a coverageData >= 17X There is a 7.87% of reference with a coverageData >= 18X There is a 5.74% of reference with a coverageData >= 19X There is a 4.15% of reference with a coverageData >= 20X There is a 2.99% of reference with a coverageData >= 21X There is a 2.17% of reference with a coverageData >= 22X There is a 1.58% of reference with a coverageData >= 23X There is a 1.17% of reference with a coverageData >= 24X There is a 0.89% of reference with a coverageData >= 25X There is a 0.69% of reference with a coverageData >= 26X There is a 0.55% of reference with a coverageData >= 27X There is a 0.46% of reference with a coverageData >= 28X There is a 0.39% of reference with a coverageData >= 29X There is a 0.35% of reference with a coverageData >= 30X There is a 0.31% of reference with a coverageData >= 31X There is a 0.29% of reference with a coverageData >= 32X There is a 0.27% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.23% of reference with a coverageData >= 35X There is a 0.22% of reference with a coverageData >= 36X There is a 0.21% of reference with a coverageData >= 37X There is a 0.2% of reference with a coverageData >= 38X There is a 0.19% of reference with a coverageData >= 39X There is a 0.19% of reference with a coverageData >= 40X There is a 0.18% of reference with a coverageData >= 41X There is a 0.17% of reference with a coverageData >= 42X There is a 0.17% of reference with a coverageData >= 43X There is a 0.16% of reference with a coverageData >= 44X There is a 0.15% of reference with a coverageData >= 45X There is a 0.15% of reference with a coverageData >= 46X There is a 0.14% of reference with a coverageData >= 47X There is a 0.14% of reference with a coverageData >= 48X There is a 0.13% of reference with a coverageData >= 49X There is a 0.13% of reference with a coverageData >= 50X There is a 0.13% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 2720207735 10.913544464147995 280.22795284445596 chr2 243199373 2809279668 11.551344205151384 68.25398839946403 chr3 198022430 2147635336 10.845414511881305 7.573913684958892 chr4 191154276 2109816338 11.037243749650674 60.154990072347616 chr5 180915260 1955897533 10.811125236201745 9.666764160047745 chr6 171115067 1880883544 10.991922435445149 58.11022633481366 chr7 159138663 1779014687 11.179022454147425 72.24240231779117 chr8 146364022 1637774186 11.189732036743292 68.87906002517035 chr9 141213431 1427250626 10.10704588007638 159.2478235535711 chr10 135534747 1639347456 12.095403520397614 137.20535961257735 chr11 135006516 1514918754 11.221078795930117 52.04832809732442 chr12 133851895 1451724618 10.84575319609782 8.751822498107844 chr13 115169878 1029437690 8.938428240759272 6.941532035891888 chr14 107349540 995044060 9.269197241087387 8.702690404050962 chr15 102531392 926988146 9.041017857243174 6.571621972358064 chr16 90354753 1051685437 11.639514271042277 60.715124975038236 chr17 81195210 968266006 11.925161669019637 66.932775068109 chr18 78077248 934068445 11.963388425268267 169.7834818139256 chr19 59128983 703413575 11.896256950673411 119.24619850616287 chr20 63025520 712359229 11.302710854269826 25.473892638325093 chr21 48129895 465573797 9.673276806442233 40.22372867348069 chr22 51304566 444498398 8.663914981758154 40.9056875951815 chrMT 16571 33424765 2017.0638464787883 280.5736582195214 chrX 155270560 863611149 5.561976133788659 20.763990776426752 chrY 59373566 309972730 5.220719435986041 82.07045222453581