BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3081183.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 = 1,720,544
number of mapped reads = 1,508,520 (87.68%)
number of supplementary alignments = 18,879 (1.1%)
number of secondary alignments = 0
number of mapped bases = 100,215,635 bp
number of sequenced bases = 100,180,901 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 58,519
duplication rate = 2.27%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.5653
>>>>>>> ACTG content
number of A's = 27,872,055 bp (27.82%)
number of C's = 19,344,773 bp (19.31%)
number of T's = 29,273,802 bp (29.22%)
number of G's = 23,661,349 bp (23.62%)
number of N's = 28,922 bp (0.03%)
GC percentage = 42.93%
>>>>>>> Mismatches and indels
general error rate = 0.009
number of mismatches = 887,841
number of insertions = 8,937
mapped reads with insertion percentage = 0.59%
number of deletions = 20,615
mapped reads with deletion percentage = 1.35%
homopolymer indels = 43.11%
>>>>>>> Coverage
mean coverageData = 0.0324X
std coverageData = 0.4538X
There is a 2.94% of reference with a coverageData >= 1X
There is a 0.16% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% 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 8104356 0.03251488789670859 0.964599698937865
chr2 243199373 8425796 0.03464563208392811 0.4682345163243953
chr3 198022430 6489110 0.0327695705986438 0.19172458912374
chr4 191154276 6270054 0.03280101356456185 0.20673849390989738
chr5 180915260 5922583 0.03273677963926316 0.19737582550266547
chr6 171115067 5774831 0.03374823211798175 0.35000832643428004
chr7 159138663 5554170 0.034901449435955106 0.6944556672482697
chr8 146364022 5043425 0.03445809244023097 0.45048921150876864
chr9 141213431 4274493 0.030269734045340207 0.4048066296521021
chr10 135534747 4717731 0.03480827687677759 0.3823156988113979
chr11 135006516 4640264 0.03437066696840025 0.4384518597077963
chr12 133851895 4482357 0.03348743773855424 0.20599997023719965
chr13 115169878 2984679 0.025915448134797885 0.16853510740092972
chr14 107349540 3003082 0.027974800823552668 0.22646413487043343
chr15 102531392 2827375 0.027575700913140825 0.1888239031715082
chr16 90354753 2942876 0.032570240106793276 0.25927402314567916
chr17 81195210 2846209 0.035053902810276615 0.2785003244486976
chr18 78077248 2684594 0.034383819470686264 0.8599413569830641
chr19 59128983 2373284 0.04013740605009222 0.6531706741622241
chr20 63025520 2050915 0.03254102465160145 0.20570224749687224
chr21 48129895 1312211 0.027263948944829405 0.21280166509485296
chr22 51304566 1215229 0.02368656622102602 0.16051555155397323
chrMT 16571 35207 2.1246152917747874 1.9085855968510537
chrX 155270560 5945090 0.03828858477743624 0.2848403748023985
chrY 59373566 295714 0.004980566604337021 0.1287494158576456