BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3124960.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,924,514
number of mapped reads = 4,665,144 (94.73%)
number of supplementary alignments = 21,408 (0.43%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 2,367,077
number of mapped paired reads (second in pair) = 2,298,067
number of mapped paired reads (both in pair) = 4,571,454
number of mapped paired reads (singletons) = 93,690
number of mapped bases = 286,174,514 bp
number of sequenced bases = 286,052,777 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 293,329
duplication rate = 3.82%
>>>>>>> Insert size
mean insert size = 92,698.1568
std insert size = 2,902,995.2107
median insert size = 165
>>>>>>> Mapping quality
mean mapping quality = 51.4236
>>>>>>> ACTG content
number of A's = 79,504,197 bp (27.79%)
number of C's = 50,917,834 bp (17.8%)
number of T's = 86,300,512 bp (30.17%)
number of G's = 69,330,234 bp (24.24%)
number of N's = 0 bp (0%)
GC percentage = 42.04%
>>>>>>> Mismatches and indels
general error rate = 0.0072
number of mismatches = 1,988,666
number of insertions = 34,154
mapped reads with insertion percentage = 0.72%
number of deletions = 74,914
mapped reads with deletion percentage = 1.59%
homopolymer indels = 46.35%
>>>>>>> Coverage
mean coverageData = 0.0924X
std coverageData = 1.04X
There is a 7.3% of reference with a coverageData >= 1X
There is a 1.19% of reference with a coverageData >= 2X
There is a 0.23% of reference with a coverageData >= 3X
There is a 0.07% 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 0.02% 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 0.01% of reference with a coverageData >= 10X
There is a 0.01% of reference with a coverageData >= 11X
There is a 0.01% of reference with a coverageData >= 12X
There is a 0.01% 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 0.01% of reference with a coverageData >= 20X
There is a 0.01% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% 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 23806389 0.09551185431148836 0.6432394089194124
chr2 243199373 25271247 0.10391164536431596 1.1219712115958687
chr3 198022430 19895338 0.10047012351075582 0.4300748379126352
chr4 191154276 17885910 0.09356793043959948 0.8048637492564648
chr5 180915260 17165483 0.09488134389547902 0.3790309546198985
chr6 171115067 16735681 0.09780366681561711 0.4508606848191481
chr7 159138663 16719460 0.10506221231731726 0.635110565519719
chr8 146364022 16147363 0.11032330745871413 0.44532878685646493
chr9 141213431 11728809 0.08305731910160868 0.6275827320149374
chr10 135534747 15939688 0.11760591547789587 3.726772757311288
chr11 135006516 12168847 0.09013525687900871 0.44257445160986914
chr12 133851895 13111824 0.09795770168214653 0.37355457548103604
chr13 115169878 8206052 0.07125172087097288 0.3080854673184609
chr14 107349540 8876230 0.08268531006280977 0.39151435125403716
chr15 102531392 7884388 0.0768973077045516 0.3406232785205253
chr16 90354753 9895977 0.10952359086189965 1.7234551567030296
chr17 81195210 6573713 0.08096183260071622 0.5884667446027332
chr18 78077248 6613848 0.08470903072813223 0.869447643459425
chr19 59128983 4210933 0.07121605659951906 0.5432701324220255
chr20 63025520 5975821 0.09481589362531241 0.4980634470188623
chr21 48129895 3457987 0.07184696746169922 0.5040329676503543
chr22 51304566 2750062 0.05360267544218189 0.32097443557939775
chrMT 16571 71576 4.31935308671776 3.4789202473226903
chrX 155270560 10528863 0.06780978312952565 0.3857384032851644
chrY 59373566 4553025 0.07668437836460758 1.702200654489043