BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1006399.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP030642/SRP030642.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 = 4,838,280
number of mapped reads = 4,233,433 (87.5%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 2,119,849
number of mapped paired reads (second in pair) = 2,113,584
number of mapped paired reads (both in pair) = 3,894,450
number of mapped paired reads (singletons) = 338,983
number of mapped bases = 163,873,023 bp
number of sequenced bases = 163,851,849 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 108,551
duplication rate = 2.04%
>>>>>>> Insert size
mean insert size = 69,564.6141
std insert size = 2,502,083.2728
median insert size = 125
>>>>>>> Mapping quality
mean mapping quality = 48.0452
>>>>>>> ACTG content
number of A's = 45,721,926 bp (27.9%)
number of C's = 35,324,046 bp (21.56%)
number of T's = 46,298,584 bp (28.26%)
number of G's = 36,500,567 bp (22.28%)
number of N's = 6,726 bp (0%)
GC percentage = 43.84%
>>>>>>> Mismatches and indels
general error rate = 0.0031
number of mismatches = 504,028
number of insertions = 4,600
mapped reads with insertion percentage = 0.11%
number of deletions = 15,734
mapped reads with deletion percentage = 0.37%
homopolymer indels = 44.03%
>>>>>>> Coverage
mean coverageData = 0.0529X
std coverageData = 0.3448X
There is a 4.57% of reference with a coverageData >= 1X
There is a 0.56% of reference with a coverageData >= 2X
There is a 0.08% 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 13557698 0.05439383840090814 0.4399966151657436
chr2 243199373 14091551 0.057942382112967046 0.3244968179126133
chr3 198022430 11028455 0.055692958620899666 0.26266847513667985
chr4 191154276 10236616 0.05355159305983822 0.2939881805349332
chr5 180915260 9657244 0.05337993047131569 0.25825197128837746
chr6 171115067 9125329 0.05332861191001959 0.27636120456885477
chr7 159138663 8736551 0.05489898454155041 0.34683662647191776
chr8 146364022 8249455 0.05636258752167934 0.7628953877836766
chr9 141213431 6814025 0.04825337754168724 0.278980533668962
chr10 135534747 7712802 0.05690645513950751 0.36233468900284566
chr11 135006516 7576457 0.056119195017224205 0.29794171786846596
chr12 133851895 7351329 0.05492136663436853 0.26345014312172976
chr13 115169878 5161579 0.044817091844101806 0.23705277965910027
chr14 107349540 5115599 0.04765366484104171 0.29996739566395764
chr15 102531392 4725525 0.04608856768471455 0.23993693632698646
chr16 90354753 4997113 0.05530548016660507 0.31158864463031405
chr17 81195210 4675078 0.057578248766152584 0.27663367322194754
chr18 78077248 4337961 0.055559860409014415 0.4104125862369532
chr19 59128983 3364906 0.056907895743784395 0.3572329165097677
chr20 63025520 3731389 0.05920441433882656 0.2951557945323759
chr21 48129895 2191926 0.04554188202571396 0.26614716159498997
chr22 51304566 2171544 0.04232652508940432 0.23971552646464817
chrMT 16571 3747 0.22611791684267696 0.8962111952002039
chrX 155270560 8765626 0.056453882822345716 0.2789840731761298
chrY 59373566 493518 0.008312082855188451 0.20957959939394616