BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR927006.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 37,455,724
number of mapped reads = 36,881,485 (98.47%)
number of supplementary alignments = 345,263 (0.92%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 18,511,251
number of mapped paired reads (second in pair) = 18,370,234
number of mapped paired reads (both in pair) = 36,517,692
number of mapped paired reads (singletons) = 363,793
number of mapped bases = 3,485,764,177 bp
number of sequenced bases = 3,483,073,558 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 3,118,190
duplication rate = 6.53%
>>>>>>> Insert size
mean insert size = 94,515.8493
std insert size = 3,015,728.2226
median insert size = 202
>>>>>>> Mapping quality
mean mapping quality = 53.5879
>>>>>>> ACTG content
number of A's = 1,008,025,331 bp (28.94%)
number of C's = 684,174,937 bp (19.64%)
number of T's = 1,022,328,817 bp (29.35%)
number of G's = 768,147,508 bp (22.05%)
number of N's = 396,965 bp (0.01%)
GC percentage = 41.7%
>>>>>>> Mismatches and indels
general error rate = 0.0093
number of mismatches = 31,528,793
number of insertions = 579,499
mapped reads with insertion percentage = 1.54%
number of deletions = 1,892,304
mapped reads with deletion percentage = 4.99%
homopolymer indels = 53.19%
>>>>>>> Coverage
mean coverageData = 1.126X
std coverageData = 4.5398X
There is a 37.72% of reference with a coverageData >= 1X
There is a 23.26% of reference with a coverageData >= 2X
There is a 14.91% of reference with a coverageData >= 3X
There is a 9.99% of reference with a coverageData >= 4X
There is a 6.86% of reference with a coverageData >= 5X
There is a 4.81% of reference with a coverageData >= 6X
There is a 3.43% of reference with a coverageData >= 7X
There is a 2.47% of reference with a coverageData >= 8X
There is a 1.8% of reference with a coverageData >= 9X
There is a 1.33% of reference with a coverageData >= 10X
There is a 0.98% of reference with a coverageData >= 11X
There is a 0.74% of reference with a coverageData >= 12X
There is a 0.55% of reference with a coverageData >= 13X
There is a 0.42% of reference with a coverageData >= 14X
There is a 0.32% of reference with a coverageData >= 15X
There is a 0.25% of reference with a coverageData >= 16X
There is a 0.19% of reference with a coverageData >= 17X
There is a 0.15% of reference with a coverageData >= 18X
There is a 0.12% of reference with a coverageData >= 19X
There is a 0.09% of reference with a coverageData >= 20X
There is a 0.08% of reference with a coverageData >= 21X
There is a 0.06% of reference with a coverageData >= 22X
There is a 0.05% of reference with a coverageData >= 23X
There is a 0.04% of reference with a coverageData >= 24X
There is a 0.04% of reference with a coverageData >= 25X
There is a 0.03% of reference with a coverageData >= 26X
There is a 0.03% of reference with a coverageData >= 27X
There is a 0.02% of reference with a coverageData >= 28X
There is a 0.02% of reference with a coverageData >= 29X
There is a 0.02% of reference with a coverageData >= 30X
There is a 0.02% of reference with a coverageData >= 31X
There is a 0.02% of reference with a coverageData >= 32X
There is a 0.02% of reference with a coverageData >= 33X
There is a 0.01% of reference with a coverageData >= 34X
There is a 0.01% of reference with a coverageData >= 35X
There is a 0.01% of reference with a coverageData >= 36X
There is a 0.01% of reference with a coverageData >= 37X
There is a 0.01% of reference with a coverageData >= 38X
There is a 0.01% of reference with a coverageData >= 39X
There is a 0.01% of reference with a coverageData >= 40X
There is a 0.01% of reference with a coverageData >= 41X
There is a 0.01% of reference with a coverageData >= 42X
There is a 0.01% of reference with a coverageData >= 43X
There is a 0.01% of reference with a coverageData >= 44X
There is a 0.01% of reference with a coverageData >= 45X
There is a 0.01% of reference with a coverageData >= 46X
There is a 0.01% of reference with a coverageData >= 47X
There is a 0.01% of reference with a coverageData >= 48X
There is a 0.01% of reference with a coverageData >= 49X
There is a 0.01% of reference with a coverageData >= 50X
There is a 0.01% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 281408566 1.1290185150631982 6.918903814722875
chr2 243199373 304773517 1.2531838106342486 7.4858783624100615
chr3 198022430 241575895 1.2199420792886948 2.327655774240793
chr4 191154276 218592030 1.143537223305431 3.287849903784045
chr5 180915260 212808618 1.1762889321774184 2.26574967739264
chr6 171115067 205520657 1.2010669814365325 3.8047433545800975
chr7 159138663 179992148 1.131039714717221 3.428977355425371
chr8 146364022 177729429 1.2142972471745823 2.7214156349896026
chr9 141213431 151376434 1.0719690961973722 5.623222258032509
chr10 135534747 166405801 1.2277722479535083 8.266204497076307
chr11 135006516 163038610 1.207635118885669 4.094106590998826
chr12 133851895 158409827 1.1834709325557176 2.3598489452002815
chr13 115169878 105191217 0.9133570237870704 1.9835283602506635
chr14 107349540 107909400 1.0052152994786936 2.2364115961545155
chr15 102531392 100459670 0.9797942663257707 2.1559977795038576
chr16 90354753 102285044 1.132038333390165 5.236380141940304
chr17 81195210 83382159 1.026934458325805 2.9366022418657605
chr18 78077248 93616696 1.1990265845435535 5.892892601780581
chr19 59128983 51615885 0.8729371347381368 3.961710398132848
chr20 63025520 81977986 1.3007109818371987 2.7060360187227417
chr21 48129895 44925040 0.9334123833014802 3.7649459822283444
chr22 51304566 43213836 0.842300001134402 2.1287609178507916
chrMT 16571 227587 13.734053466900006 12.737296717297777
chrX 155270560 202682195 1.3053485155202635 2.852979710355524
chrY 59373566 6645930 0.11193415601818493 4.057554887743841