BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR2094122.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 = 484,064
number of mapped reads = 457,703 (94.55%)
number of supplementary alignments = 1,156 (0.24%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 229,494
number of mapped paired reads (second in pair) = 228,209
number of mapped paired reads (both in pair) = 455,788
number of mapped paired reads (singletons) = 1,915
number of mapped bases = 68,016,731 bp
number of sequenced bases = 67,952,082 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 456,280
duplication rate = 46.53%
>>>>>>> Insert size
mean insert size = 5,980.3536
std insert size = 893,051.4558
median insert size = 237
>>>>>>> Mapping quality
mean mapping quality = 12.8285
>>>>>>> ACTG content
number of A's = 18,865,115 bp (27.76%)
number of C's = 14,643,394 bp (21.55%)
number of T's = 19,388,138 bp (28.53%)
number of G's = 15,054,573 bp (22.15%)
number of N's = 862 bp (0%)
GC percentage = 43.7%
>>>>>>> Mismatches and indels
general error rate = 0.0161
number of mismatches = 1,068,827
number of insertions = 18,175
mapped reads with insertion percentage = 3.93%
number of deletions = 48,387
mapped reads with deletion percentage = 10.35%
homopolymer indels = 68.06%
>>>>>>> Coverage
mean coverageData = 0.022X
std coverageData = 39.7308X
There is a 0% of reference with a coverageData >= 1X
There is a 0% of reference with a coverageData >= 2X
There is a 0% of reference with a coverageData >= 3X
There is a 0% of reference with a coverageData >= 4X
There is a 0% of reference with a coverageData >= 5X
There is a 0% of reference with a coverageData >= 6X
There is a 0% of reference with a coverageData >= 7X
There is a 0% of reference with a coverageData >= 8X
There is a 0% of reference with a coverageData >= 9X
There is a 0% of reference with a coverageData >= 10X
There is a 0% of reference with a coverageData >= 11X
There is a 0% of reference with a coverageData >= 12X
There is a 0% of reference with a coverageData >= 13X
There is a 0% of reference with a coverageData >= 14X
There is a 0% of reference with a coverageData >= 15X
There is a 0% 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 30180 1.2108294807417952E-4 0.12281798200995833
chr2 243199373 164413 6.760420389735133E-4 0.6305352701346877
chr3 198022430 3718 1.8775650818950156E-5 0.005994999703122061
chr4 191154276 5578 2.9180618486399958E-5 0.012080083410679883
chr5 180915260 6667 3.685150716418283E-5 0.022157318575852993
chr6 171115067 38567 2.2538634777263653E-4 0.22656848558214912
chr7 159138663 10030 6.302679569451957E-5 0.04274173218530627
chr8 146364022 8490 5.800605834677049E-5 0.03688053677275614
chr9 141213431 20360 1.441789202048352E-4 0.13909438008061545
chr10 135534747 4226 3.1180196175081215E-5 0.013818601753358827
chr11 135006516 17317 1.2826788301092075E-4 0.09594928419563259
chr12 133851895 3721 2.7799382294886448E-5 0.01123247672477086
chr13 115169878 1698 1.474343838412332E-5 0.0047421832770484975
chr14 107349540 55277 5.149253550597422E-4 0.29909149541216634
chr15 102531392 1871 1.8248069820411685E-5 0.006700241400408211
chr16 90354753 3146 3.4818312214300445E-5 0.012400867885540736
chr17 81195210 2863 3.52607007236018E-5 0.009874437126322569
chr18 78077248 1554 1.990336544648705E-5 0.00475316962028397
chr19 59128983 980 1.6573936338461968E-5 0.005279299310018954
chr20 63025520 562 8.917022818693127E-6 0.004819606442803519
chr21 48129895 2389 4.9636509699429016E-5 0.02013713838483067
chr22 51304566 847 1.6509251827605363E-5 0.004636678890717111
chrMT 16571 67042078 4045.747269325931 16688.566405432324
chrX 155270560 585572 0.0037713008827945232 1.9054512768372525
chrY 59373566 4627 7.793030319250152E-5 0.02783099487824044