BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR611511.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP017032/SRP017032.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 = 1,127,379,558
number of mapped reads = 1,098,821,716 (97.47%)
number of supplementary alignments = 11,016,486 (0.98%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 551,187,316
number of mapped paired reads (second in pair) = 547,634,400
number of mapped paired reads (both in pair) = 1,087,372,276
number of mapped paired reads (singletons) = 11,449,440
number of mapped bases = 94,927,579,197 bp
number of sequenced bases = 94,854,275,347 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 436,311,124
duplication rate = 31.78%
>>>>>>> Insert size
mean insert size = 146,464.4709
std insert size = 3,658,832.9819
median insert size = 187
>>>>>>> Mapping quality
mean mapping quality = 52.067
>>>>>>> ACTG content
number of A's = 27,033,387,773 bp (28.5%)
number of C's = 19,803,216,610 bp (20.88%)
number of T's = 27,160,715,864 bp (28.63%)
number of G's = 20,848,652,970 bp (21.98%)
number of N's = 8,302,130 bp (0.01%)
GC percentage = 42.86%
>>>>>>> Mismatches and indels
general error rate = 0.0111
number of mismatches = 1,014,370,303
number of insertions = 17,479,762
mapped reads with insertion percentage = 1.55%
number of deletions = 44,345,302
mapped reads with deletion percentage = 3.94%
homopolymer indels = 48.19%
>>>>>>> Coverage
mean coverageData = 30.6644X
std coverageData = 352.999X
There is a 86.82% of reference with a coverageData >= 1X
There is a 83.38% of reference with a coverageData >= 2X
There is a 80.12% of reference with a coverageData >= 3X
There is a 76.99% of reference with a coverageData >= 4X
There is a 73.99% of reference with a coverageData >= 5X
There is a 71.11% of reference with a coverageData >= 6X
There is a 68.36% of reference with a coverageData >= 7X
There is a 65.74% of reference with a coverageData >= 8X
There is a 63.23% of reference with a coverageData >= 9X
There is a 60.85% of reference with a coverageData >= 10X
There is a 58.57% of reference with a coverageData >= 11X
There is a 56.41% of reference with a coverageData >= 12X
There is a 54.34% of reference with a coverageData >= 13X
There is a 52.38% of reference with a coverageData >= 14X
There is a 50.5% of reference with a coverageData >= 15X
There is a 48.71% of reference with a coverageData >= 16X
There is a 47.01% of reference with a coverageData >= 17X
There is a 45.38% of reference with a coverageData >= 18X
There is a 43.83% of reference with a coverageData >= 19X
There is a 42.34% of reference with a coverageData >= 20X
There is a 40.92% of reference with a coverageData >= 21X
There is a 39.57% of reference with a coverageData >= 22X
There is a 38.27% of reference with a coverageData >= 23X
There is a 37.03% of reference with a coverageData >= 24X
There is a 35.85% of reference with a coverageData >= 25X
There is a 34.71% of reference with a coverageData >= 26X
There is a 33.62% of reference with a coverageData >= 27X
There is a 32.57% of reference with a coverageData >= 28X
There is a 31.57% of reference with a coverageData >= 29X
There is a 30.6% of reference with a coverageData >= 30X
There is a 29.68% of reference with a coverageData >= 31X
There is a 28.79% of reference with a coverageData >= 32X
There is a 27.94% of reference with a coverageData >= 33X
There is a 27.11% of reference with a coverageData >= 34X
There is a 26.32% of reference with a coverageData >= 35X
There is a 25.56% of reference with a coverageData >= 36X
There is a 24.83% of reference with a coverageData >= 37X
There is a 24.13% of reference with a coverageData >= 38X
There is a 23.45% of reference with a coverageData >= 39X
There is a 22.79% of reference with a coverageData >= 40X
There is a 22.16% of reference with a coverageData >= 41X
There is a 21.55% of reference with a coverageData >= 42X
There is a 20.97% of reference with a coverageData >= 43X
There is a 20.4% of reference with a coverageData >= 44X
There is a 19.85% of reference with a coverageData >= 45X
There is a 19.32% of reference with a coverageData >= 46X
There is a 18.81% of reference with a coverageData >= 47X
There is a 18.32% of reference with a coverageData >= 48X
There is a 17.84% of reference with a coverageData >= 49X
There is a 17.38% of reference with a coverageData >= 50X
There is a 16.93% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 6538059395 26.230865017584048 348.68705171702476
chr2 243199373 9522729682 39.1560618127087 465.23990215245635
chr3 198022430 7016714299 35.43393694845579 59.79773059396615
chr4 191154276 4938327451 25.8342505035043 301.3185887610142
chr5 180915260 5641038305 31.180555498745655 56.21979399086808
chr6 171115067 4267230227 24.93778193711019 129.8944299829517
chr7 159138663 6596649607 41.45221206866618 306.1310985669156
chr8 146364022 3927451446 26.833448495969865 128.48685681199905
chr9 141213431 3872990718 27.426503913781403 419.5127867971833
chr10 135534747 4659795663 34.3808194292789 1110.9244881479208
chr11 135006516 5199623514 38.513870797169524 213.12343624121252
chr12 133851895 4091002918 30.56365334237517 54.384880210649975
chr13 115169878 3401145609 29.531555195361065 47.301372362762216
chr14 107349540 2729523972 25.426508320389637 68.13012052905782
chr15 102531392 2262167947 22.06317404722253 35.09458396618977
chr16 90354753 3003986818 33.24658325389922 497.89302271912544
chr17 81195210 3215318025 39.599848624075236 246.60543804279015
chr18 78077248 1729678368 22.153423850184883 442.1528201428339
chr19 59128983 1757752866 29.727432754931705 199.33387388596483
chr20 63025520 3361609340 53.337272584184944 151.08711536586517
chr21 48129895 1461327806 30.362164845778285 181.1761890498766
chr22 51304566 1041788261 20.30595602348532 57.86633414322501
chrMT 16571 84646800 5108.128658499789 2028.522982412096
chrX 155270560 4175832244 26.893908568372524 119.20106848468893
chrY 59373566 431187916 7.262287665187569 475.27546762691617