BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3080706.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 = 1,982,222
number of mapped reads = 1,707,050 (86.12%)
number of supplementary alignments = 15,739 (0.79%)
number of secondary alignments = 0
number of mapped bases = 116,032,910 bp
number of sequenced bases = 115,989,939 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 96,938
duplication rate = 4.78%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.0366
>>>>>>> ACTG content
number of A's = 33,591,811 bp (28.96%)
number of C's = 21,383,616 bp (18.44%)
number of T's = 36,388,410 bp (31.37%)
number of G's = 24,624,471 bp (21.23%)
number of N's = 1,631 bp (0%)
GC percentage = 39.67%
>>>>>>> Mismatches and indels
general error rate = 0.0083
number of mismatches = 948,758
number of insertions = 9,001
mapped reads with insertion percentage = 0.52%
number of deletions = 24,448
mapped reads with deletion percentage = 1.42%
homopolymer indels = 47.25%
>>>>>>> Coverage
mean coverageData = 0.0375X
std coverageData = 0.3423X
There is a 2.93% of reference with a coverageData >= 1X
There is a 0.6% of reference with a coverageData >= 2X
There is a 0.13% of reference with a coverageData >= 3X
There is a 0.03% 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 9165023 0.036770311597338005 0.5080031989494175
chr2 243199373 10190227 0.0419007124660638 0.3484680369293336
chr3 198022430 8193107 0.0413746412464487 0.24923711891716835
chr4 191154276 8070434 0.04221947930686102 0.26347137170044926
chr5 180915260 6709705 0.03708755690371282 0.2372244024675015
chr6 171115067 6334737 0.03702033439287962 0.24642747533359294
chr7 159138663 6794157 0.04269331457183349 0.4967638677599715
chr8 146364022 6317012 0.0431595956006183 0.7072727388789118
chr9 141213431 4003464 0.028350447770084986 0.26570244196284903
chr10 135534747 5346508 0.0394475078778138 0.29854764082827007
chr11 135006516 5393612 0.03995075319179409 0.2815729184123203
chr12 133851895 5263976 0.039326869447757914 0.2448408433371279
chr13 115169878 3684905 0.03199538858589396 0.21976017366548303
chr14 107349540 3597972 0.03351641749000508 0.23471679387891337
chr15 102531392 3237643 0.03157709006818127 0.21916843390781524
chr16 90354753 3178694 0.035180152614661016 0.23982478619529607
chr17 81195210 2686523 0.033087210440123256 0.23306479530982027
chr18 78077248 3109603 0.039827261842015745 0.4294935259526916
chr19 59128983 1989406 0.03364519224015742 0.3583418043089913
chr20 63025520 2363234 0.03749646175073208 0.23946046017545652
chr21 48129895 1571277 0.032646591063620646 0.2323480103813417
chr22 51304566 1237884 0.024128144851668757 0.1870602820186189
chrMT 16571 44474 2.6838452718604793 2.3269703760494562
chrX 155270560 7243725 0.04665227587251569 0.2780199929058048
chrY 59373566 305608 0.0051472064184253305 0.12997077227889578