BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1818951.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,731,536
number of mapped reads = 1,660,237 (95.88%)
number of supplementary alignments = 22,000 (1.27%)
number of secondary alignments = 0
number of mapped bases = 153,601,475 bp
number of sequenced bases = 153,512,621 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 585,651
duplication rate = 30.08%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 49.2985
>>>>>>> ACTG content
number of A's = 44,948,605 bp (29.28%)
number of C's = 32,249,768 bp (21.01%)
number of T's = 44,358,338 bp (28.9%)
number of G's = 31,949,555 bp (20.81%)
number of N's = 6,355 bp (0%)
GC percentage = 41.82%
>>>>>>> Mismatches and indels
general error rate = 0.0068
number of mismatches = 994,967
number of insertions = 21,801
mapped reads with insertion percentage = 1.27%
number of deletions = 47,935
mapped reads with deletion percentage = 2.82%
homopolymer indels = 41.69%
>>>>>>> Coverage
mean coverageData = 0.0496X
std coverageData = 0.5758X
There is a 2.74% of reference with a coverageData >= 1X
There is a 1.11% of reference with a coverageData >= 2X
There is a 0.5% of reference with a coverageData >= 3X
There is a 0.24% of reference with a coverageData >= 4X
There is a 0.12% of reference with a coverageData >= 5X
There is a 0.06% of reference with a coverageData >= 6X
There is a 0.03% of reference with a coverageData >= 7X
There is a 0.02% 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% 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 18070071 0.07249759670608805 0.9590325165698768
chr2 243199373 13777155 0.05664963206956952 0.9520982716861417
chr3 198022430 10060739 0.050806057677405536 0.36698487396204743
chr4 191154276 10163386 0.0531684993538936 0.4303466276217587
chr5 180915260 7899629 0.043664801963084816 0.35588481243151554
chr6 171115067 8239558 0.04815214781758523 0.3892293989022293
chr7 159138663 7759397 0.04875871679278844 0.44457734877500366
chr8 146364022 9851648 0.06730921892813249 0.47133643106712314
chr9 141213431 5761744 0.04080167133677249 0.5714411089312887
chr10 135534747 7614691 0.05618257434752138 0.7089134512485139
chr11 135006516 5898555 0.04369089118631874 0.3803393765620739
chr12 133851895 7043913 0.05262467894085474 0.3819113934648379
chr13 115169878 2489902 0.0216193855827476 0.23572608789403907
chr14 107349540 3705738 0.03452029696634005 0.35374980444088205
chr15 102531392 4466935 0.04356651083016604 0.3462714704240911
chr16 90354753 4459292 0.04935315356348769 0.6949977905502375
chr17 81195210 3329913 0.04101120004492876 0.37348892167792636
chr18 78077248 3834384 0.04911013257024633 0.7402272089399332
chr19 59128983 2307325 0.039021895573614046 0.7572992545987587
chr20 63025520 3278703 0.05202183179131247 0.3902623677919862
chr21 48129895 2023421 0.04204083553475444 0.35744991119549097
chr22 51304566 1836761 0.03580112148302746 0.32946610744329907
chrMT 16571 145838 8.800796572325146 6.563292918276182
chrX 155270560 9098776 0.05859949239572524 0.4948258614804722
chrY 59373566 484001 0.008151792668137871 0.6207026398311114