BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3081914.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 = 2,772,111
number of mapped reads = 2,579,429 (93.05%)
number of supplementary alignments = 21,702 (0.78%)
number of secondary alignments = 0
number of mapped bases = 177,014,626 bp
number of sequenced bases = 176,949,377 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 91,289
duplication rate = 2.75%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.9452
>>>>>>> ACTG content
number of A's = 50,606,984 bp (28.6%)
number of C's = 33,070,519 bp (18.69%)
number of T's = 55,607,155 bp (31.43%)
number of G's = 37,662,617 bp (21.28%)
number of N's = 2,102 bp (0%)
GC percentage = 39.97%
>>>>>>> Mismatches and indels
general error rate = 0.0085
number of mismatches = 1,483,618
number of insertions = 14,229
mapped reads with insertion percentage = 0.55%
number of deletions = 39,424
mapped reads with deletion percentage = 1.51%
homopolymer indels = 47.86%
>>>>>>> Coverage
mean coverageData = 0.0572X
std coverageData = 0.4117X
There is a 4.85% of reference with a coverageData >= 1X
There is a 0.64% of reference with a coverageData >= 2X
There is a 0.11% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% 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 13563295 0.0544162937110596 0.6518869166586381
chr2 243199373 15703268 0.06456952502093827 0.49674350361387276
chr3 198022430 11801865 0.059598627286817966 0.2795087615756742
chr4 191154276 12695858 0.06641681402931317 0.31574820985725593
chr5 180915260 10529814 0.05820301725791401 0.27473410546403526
chr6 171115067 9976521 0.058302995609381375 0.31154365848478005
chr7 159138663 9794895 0.06154943629254947 0.5155066383023702
chr8 146364022 9073066 0.061989728596007015 0.5625549021155082
chr9 141213431 7605569 0.05385868005713989 0.39355540641642517
chr10 135534747 8729292 0.06440630313051753 0.45732594653233055
chr11 135006516 8285933 0.061374319147677284 0.3772331433553335
chr12 133851895 8141097 0.06082167906550744 0.28239303358063855
chr13 115169878 5741989 0.049856690826745514 0.25539611383298516
chr14 107349540 5384838 0.05016172402788126 0.27340050940171484
chr15 102531392 5120798 0.049943708947207115 0.2567675113600182
chr16 90354753 4977770 0.055091401777170486 0.3039560156308374
chr17 81195210 4099948 0.050494949147862296 0.27896132149022046
chr18 78077248 4519625 0.05788658176066861 0.7416733080760489
chr19 59128983 2785607 0.047110686818340845 0.5201009033636101
chr20 63025520 3346837 0.053102885942075524 0.27241967882953255
chr21 48129895 2274430 0.04725607649881638 0.2688180366572728
chr22 51304566 1789094 0.0348720228916857 0.20922520681213552
chrMT 16571 11493 0.6935610403717337 0.9877860459302394
chrX 155270560 10609139 0.06832679034583246 0.32814172032946554
chrY 59373566 452585 0.007622668310001794 0.18006706495654795