BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6238055.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 = 1,337,472
number of mapped reads = 991,760 (74.15%)
number of supplementary alignments = 10,899 (0.81%)
number of secondary alignments = 0
number of mapped bases = 65,209,356 bp
number of sequenced bases = 65,180,968 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 247,818
duplication rate = 14.08%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.4751
>>>>>>> ACTG content
number of A's = 17,603,244 bp (27.01%)
number of C's = 12,290,077 bp (18.86%)
number of T's = 20,482,789 bp (31.42%)
number of G's = 14,796,658 bp (22.7%)
number of N's = 8,200 bp (0.01%)
GC percentage = 41.56%
>>>>>>> Mismatches and indels
general error rate = 0.0088
number of mismatches = 567,384
number of insertions = 4,847
mapped reads with insertion percentage = 0.49%
number of deletions = 15,965
mapped reads with deletion percentage = 1.6%
homopolymer indels = 46.13%
>>>>>>> Coverage
mean coverageData = 0.0211X
std coverageData = 0.7002X
There is a 0.63% of reference with a coverageData >= 1X
There is a 0.34% of reference with a coverageData >= 2X
There is a 0.25% of reference with a coverageData >= 3X
There is a 0.19% of reference with a coverageData >= 4X
There is a 0.14% of reference with a coverageData >= 5X
There is a 0.11% of reference with a coverageData >= 6X
There is a 0.08% of reference with a coverageData >= 7X
There is a 0.06% of reference with a coverageData >= 8X
There is a 0.05% of reference with a coverageData >= 9X
There is a 0.04% of reference with a coverageData >= 10X
There is a 0.03% of reference with a coverageData >= 11X
There is a 0.02% of reference with a coverageData >= 12X
There is a 0.02% of reference with a coverageData >= 13X
There is a 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% 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 13335323 0.05350166409414884 1.6068783623975134
chr2 243199373 3062042 0.012590665683994176 0.4232138608781522
chr3 198022430 2093552 0.010572297289756519 0.2787006516768368
chr4 191154276 2706243 0.014157376212708944 0.3225631202000259
chr5 180915260 3242477 0.017922628527853316 0.3508279927414519
chr6 171115067 1897157 0.011087024849775503 0.2804676062163059
chr7 159138663 10187965 0.0640194205979976 1.36639088133748
chr8 146364022 1567598 0.010710268675180297 0.30568387939598657
chr9 141213431 1683955 0.011924892611666663 0.3335265311703895
chr10 135534747 1766082 0.013030474023019352 0.5684393671816916
chr11 135006516 1813582 0.013433292360496141 0.3440586060512598
chr12 133851895 2063659 0.015417480641570296 0.3183786997932993
chr13 115169878 1090471 0.009468369845802911 0.2606603842968722
chr14 107349540 989458 0.009217161060960299 0.2938149370901452
chr15 102531392 1042597 0.010168563789712325 0.30185590409325985
chr16 90354753 5708797 0.06318203315768015 0.6945174156199012
chr17 81195210 757127 0.009324774207739594 0.2514503528295049
chr18 78077248 1772842 0.022706256245097162 0.9341677830214393
chr19 59128983 1079878 0.018263091046230237 1.4232257222821327
chr20 63025520 689695 0.010943106855762554 0.2960913414972408
chr21 48129895 3226208 0.06703127027391188 0.6972407505117667
chr22 51304566 644753 0.012567166049119293 0.31246720900973257
chrMT 16571 705040 42.54661758493754 32.31408468406886
chrX 155270560 1942820 0.012512481438850996 0.29870701919615916
chrY 59373566 140035 0.002358541173019657 0.11190208473914653