BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6063530.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 6,410,657
number of mapped reads = 5,834,948 (91.02%)
number of supplementary alignments = 62,793 (0.98%)
number of secondary alignments = 0
number of mapped bases = 369,067,505 bp
number of sequenced bases = 368,926,789 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,173,603
duplication rate = 15.57%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.9612
>>>>>>> ACTG content
number of A's = 96,404,947 bp (26.13%)
number of C's = 68,390,820 bp (18.54%)
number of T's = 117,164,582 bp (31.76%)
number of G's = 86,924,609 bp (23.56%)
number of N's = 41,831 bp (0.01%)
GC percentage = 42.1%
>>>>>>> Mismatches and indels
general error rate = 0.0055
number of mismatches = 1,987,899
number of insertions = 23,778
mapped reads with insertion percentage = 0.4%
number of deletions = 80,612
mapped reads with deletion percentage = 1.37%
homopolymer indels = 43.86%
>>>>>>> Coverage
mean coverageData = 0.1192X
std coverageData = 1.1062X
There is a 6.71% of reference with a coverageData >= 1X
There is a 2.67% of reference with a coverageData >= 2X
There is a 1.18% of reference with a coverageData >= 3X
There is a 0.55% of reference with a coverageData >= 4X
There is a 0.27% of reference with a coverageData >= 5X
There is a 0.14% of reference with a coverageData >= 6X
There is a 0.07% of reference with a coverageData >= 7X
There is a 0.04% of reference with a coverageData >= 8X
There is a 0.03% of reference with a coverageData >= 9X
There is a 0.02% 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% 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 34251679 0.137418630543753 2.241295818810548
chr2 243199373 32708867 0.13449404328850798 1.7696142704672673
chr3 198022430 12753173 0.0644026689299793 0.41502318528495974
chr4 191154276 26086812 0.13646993698430268 0.6889072478983074
chr5 180915260 15583244 0.08613559740621106 0.47984528120738484
chr6 171115067 27200949 0.15896291002825602 0.7976084247239856
chr7 159138663 29568307 0.18580215795830834 1.415591690233226
chr8 146364022 17863297 0.12204704924001064 1.0051907088459262
chr9 141213431 11952614 0.08464218959455776 0.866349571518811
chr10 135534747 19563995 0.14434671132709606 0.8681247466747352
chr11 135006516 19691712 0.14585749327832442 0.7640978930743464
chr12 133851895 19481464 0.1455449248589271 0.6627051208875967
chr13 115169878 8596056 0.07463805770463697 0.4811079734398474
chr14 107349540 1846743 0.01720308256560764 0.4275786541443819
chr15 102531392 5970317 0.058229161660069924 0.4477453431611352
chr16 90354753 9834717 0.1088455966450376 0.5860091272840071
chr17 81195210 13643727 0.16803610705606895 0.721760678803776
chr18 78077248 11001497 0.14090528651829531 1.575804990960969
chr19 59128983 7002815 0.11843286734696587 1.4967558147724591
chr20 63025520 5439709 0.08630962505347041 0.5526866098425223
chr21 48129895 5450880 0.11325351946020244 0.5855503221277097
chr22 51304566 5320675 0.10370763101280303 0.5100586138028429
chrMT 16571 818927 49.419286705690666 31.137617500338767
chrX 155270560 26473351 0.1704982000451341 0.8000365788945958
chrY 59373566 961978 0.016202126043768368 0.4003725843513644