BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR2094110.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 407,496
number of mapped reads = 390,342 (95.79%)
number of supplementary alignments = 31,874 (7.82%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 196,154
number of mapped paired reads (second in pair) = 194,188
number of mapped paired reads (both in pair) = 387,314
number of mapped paired reads (singletons) = 3,028
number of mapped bases = 48,832,320 bp
number of sequenced bases = 47,942,182 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 378,003
duplication rate = 52.81%
>>>>>>> Insert size
mean insert size = 1,840,455.4839
std insert size = 11,841,008.4515
median insert size = 149
>>>>>>> Mapping quality
mean mapping quality = 40.4159
>>>>>>> ACTG content
number of A's = 13,935,673 bp (29.07%)
number of C's = 10,237,019 bp (21.35%)
number of T's = 12,950,637 bp (27.01%)
number of G's = 10,818,160 bp (22.57%)
number of N's = 693 bp (0%)
GC percentage = 43.92%
>>>>>>> Mismatches and indels
general error rate = 0.0349
number of mismatches = 1,602,207
number of insertions = 32,073
mapped reads with insertion percentage = 8.09%
number of deletions = 124,465
mapped reads with deletion percentage = 31.02%
homopolymer indels = 29.21%
>>>>>>> Coverage
mean coverageData = 0.0158X
std coverageData = 3.3458X
There is a 0.02% of reference with a coverageData >= 1X
There is a 0.01% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0.01% 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 0.01% of reference with a coverageData >= 7X
There is a 0.01% of reference with a coverageData >= 8X
There is a 0.01% of reference with a coverageData >= 9X
There is a 0.01% 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 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% of reference with a coverageData >= 19X
There is a 0.01% of reference with a coverageData >= 20X
There is a 0.01% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% of reference with a coverageData >= 23X
There is a 0.01% of reference with a coverageData >= 24X
There is a 0.01% of reference with a coverageData >= 25X
There is a 0.01% of reference with a coverageData >= 26X
There is a 0.01% of reference with a coverageData >= 27X
There is a 0.01% of reference with a coverageData >= 28X
There is a 0.01% of reference with a coverageData >= 29X
There is a 0.01% of reference with a coverageData >= 30X
There is a 0.01% of reference with a coverageData >= 31X
There is a 0.01% of reference with a coverageData >= 32X
There is a 0.01% 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% 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 1093795 0.004388334101683141 1.5096601905120783
chr2 243199373 2199131 0.009042502753491884 2.727642967920794
chr3 198022430 832531 0.004204225753617911 1.2697879494625557
chr4 191154276 1631096 0.00853287739166243 2.5161381056178294
chr5 180915260 1228692 0.006791533229424649 2.950254367554851
chr6 171115067 1081484 0.0063202149229792835 2.1370287786549023
chr7 159138663 1498311 0.009415128742158654 2.5328766840368053
chr8 146364022 952238 0.006505956771261724 1.6691240991533773
chr9 141213431 839249 0.005943124489341244 2.20602548163104
chr10 135534747 1140537 0.008415089305475297 2.820615913104076
chr11 135006516 2018197 0.014948885874515865 3.738001031944277
chr12 133851895 1445699 0.01080073614198738 3.0386700519649765
chr13 115169878 863660 0.0074990094198068005 2.032795970771851
chr14 107349540 255761 0.0023825067159114048 0.8030884506913523
chr15 102531392 748481 0.007300017930118417 1.9344766775866242
chr16 90354753 249535 0.0027617252188161037 1.037541102558857
chr17 81195210 557873 0.006870762450149461 1.923596497327201
chr18 78077248 305688 0.003915199470145259 1.3750941213539505
chr19 59128983 48412 8.187524551200213E-4 0.2028286913968285
chr20 63025520 121352 0.0019254422652919007 0.5504467888917594
chr21 48129895 102226 0.0021239605862427083 0.4862940899856226
chr22 51304566 44254 8.62574297967943E-4 0.2279108252885911
chrMT 16571 172246 10.394423993723976 61.32432779819767
chrX 155270560 28151904 0.1813087039809736 11.204156723992208
chrY 59373566 1249968 0.021052601085136104 4.115044923842557