BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR5038395.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 12,873,080
number of mapped reads = 12,592,388 (97.82%)
number of supplementary alignments = 255,525 (1.98%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 6,348,643
number of mapped paired reads (second in pair) = 6,243,745
number of mapped paired reads (both in pair) = 12,468,872
number of mapped paired reads (singletons) = 123,516
number of mapped bases = 1,807,742,100 bp
number of sequenced bases = 1,806,328,453 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 2,180,550
duplication rate = 9.61%
>>>>>>> Insert size
mean insert size = 76,243.8796
std insert size = 2,518,233.8885
median insert size = 260
>>>>>>> Mapping quality
mean mapping quality = 53.7505
>>>>>>> ACTG content
number of A's = 544,078,927 bp (30.12%)
number of C's = 354,045,871 bp (19.6%)
number of T's = 544,347,030 bp (30.14%)
number of G's = 363,818,813 bp (20.14%)
number of N's = 37,812 bp (0%)
GC percentage = 39.74%
>>>>>>> Mismatches and indels
general error rate = 0.0151
number of mismatches = 26,050,732
number of insertions = 374,880
mapped reads with insertion percentage = 2.79%
number of deletions = 670,719
mapped reads with deletion percentage = 5.11%
homopolymer indels = 46.83%
>>>>>>> Coverage
mean coverageData = 0.584X
std coverageData = 11.2618X
There is a 25.37% of reference with a coverageData >= 1X
There is a 12.93% of reference with a coverageData >= 2X
There is a 6.32% of reference with a coverageData >= 3X
There is a 3.48% of reference with a coverageData >= 4X
There is a 1.87% of reference with a coverageData >= 5X
There is a 1.07% of reference with a coverageData >= 6X
There is a 0.61% of reference with a coverageData >= 7X
There is a 0.37% of reference with a coverageData >= 8X
There is a 0.23% of reference with a coverageData >= 9X
There is a 0.15% of reference with a coverageData >= 10X
There is a 0.1% of reference with a coverageData >= 11X
There is a 0.08% of reference with a coverageData >= 12X
There is a 0.06% of reference with a coverageData >= 13X
There is a 0.05% of reference with a coverageData >= 14X
There is a 0.04% of reference with a coverageData >= 15X
There is a 0.04% of reference with a coverageData >= 16X
There is a 0.03% of reference with a coverageData >= 17X
There is a 0.03% of reference with a coverageData >= 18X
There is a 0.03% of reference with a coverageData >= 19X
There is a 0.03% of reference with a coverageData >= 20X
There is a 0.02% of reference with a coverageData >= 21X
There is a 0.02% of reference with a coverageData >= 22X
There is a 0.02% of reference with a coverageData >= 23X
There is a 0.02% of reference with a coverageData >= 24X
There is a 0.02% of reference with a coverageData >= 25X
There is a 0.02% of reference with a coverageData >= 26X
There is a 0.02% 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 0.02% of reference with a coverageData >= 34X
There is a 0.02% of reference with a coverageData >= 35X
There is a 0.02% of reference with a coverageData >= 36X
There is a 0.02% of reference with a coverageData >= 37X
There is a 0.02% of reference with a coverageData >= 38X
There is a 0.02% of reference with a coverageData >= 39X
There is a 0.02% of reference with a coverageData >= 40X
There is a 0.02% of reference with a coverageData >= 41X
There is a 0.02% of reference with a coverageData >= 42X
There is a 0.02% of reference with a coverageData >= 43X
There is a 0.02% 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 113160167 0.454001544894847 15.134675873863777
chr2 243199373 170772231 0.7021902601697908 13.747129471256137
chr3 198022430 126663030 0.6396398125202282 1.4293788330760515
chr4 191154276 124345561 0.6504984539294324 13.17584350859226
chr5 180915260 110937006 0.6131987207712606 1.4847394087330394
chr6 171115067 106485191 0.6223016644115856 13.207470567521622
chr7 159138663 137255026 0.8624869872131576 11.952052628873163
chr8 146364022 86200946 0.5889490109803077 3.0794741416919167
chr9 141213431 77398069 0.5480928297818923 19.13915319499663
chr10 135534747 82890756 0.6115830651161359 22.886418336090586
chr11 135006516 81538340 0.603958552637563 7.016907001538278
chr12 133851895 64745181 0.4837076157943076 1.2274545580442602
chr13 115169878 114235609 0.9918879049259738 1.8021171398828846
chr14 107349540 34462035 0.321026387257924 1.1347134123073876
chr15 102531392 30558427 0.2980397164606914 0.8763827840457881
chr16 90354753 66014572 0.7306153778097318 15.580681283379317
chr17 81195210 37251311 0.45878705160070404 5.624261860565163
chr18 78077248 31666812 0.4055830963714295 14.202773588237074
chr19 59128983 20390983 0.34485597359251047 8.47083835906106
chr20 63025520 52132729 0.8271685660031047 4.0331650847769245
chr21 48129895 17273353 0.3588903113127506 5.729422464207392
chr22 51304566 8420269 0.1641231893473185 0.7281960527875092
chrMT 16571 2417062 145.860961921429 88.52488112987206
chrX 155270560 72087197 0.4642682875620465 2.1320907736866377
chrY 59373566 38440237 0.6474301543552227 19.704677172787175