BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR2094019.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 = 26,194
number of mapped reads = 15,102 (57.65%)
number of supplementary alignments = 24 (0.09%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 7,533
number of mapped paired reads (second in pair) = 7,569
number of mapped paired reads (both in pair) = 14,894
number of mapped paired reads (singletons) = 208
number of mapped bases = 2,227,069 bp
number of sequenced bases = 2,225,796 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 14,651
duplication rate = 32.42%
>>>>>>> Insert size
mean insert size = 7,954.8245
std insert size = 614,744.4547
median insert size = 217
>>>>>>> Mapping quality
mean mapping quality = 7.4763
>>>>>>> ACTG content
number of A's = 644,270 bp (28.95%)
number of C's = 444,467 bp (19.97%)
number of T's = 656,905 bp (29.51%)
number of G's = 480,141 bp (21.57%)
number of N's = 13 bp (0%)
GC percentage = 41.54%
>>>>>>> Mismatches and indels
general error rate = 0.0176
number of mismatches = 38,898
number of insertions = 152
mapped reads with insertion percentage = 0.92%
number of deletions = 975
mapped reads with deletion percentage = 6.36%
homopolymer indels = 74.36%
>>>>>>> Coverage
mean coverageData = 0.0007X
std coverageData = 1.682X
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 1976 7.927763598229912E-6 0.0040309606385326
chr2 243199373 16078 6.611036780921306E-5 0.06396807096506543
chr3 198022430 606 3.060259385767562E-6 0.0024223981417919086
chr4 191154276 1394 7.292538933316877E-6 0.005464968043067709
chr5 180915260 1450 8.01480206810636E-6 0.004066702275582214
chr6 171115067 2854 1.6678835184046066E-5 0.0068405260071413366
chr7 159138663 653 4.103339739633228E-6 0.0022421076268943855
chr8 146364022 183 1.2503072647183746E-6 0.0011181706942368496
chr9 141213431 344 2.436028907193679E-6 0.0019299879435936958
chr10 135534747 1303 9.613770850953814E-6 0.006171989983469614
chr11 135006516 688 5.096050326933849E-6 0.002961405258408467
chr12 133851895 844 6.3054766613502184E-6 0.0033864227791893793
chr13 115169878 1549 1.3449697324503548E-5 0.00879468226967203
chr14 107349540 3763 3.505371331819401E-5 0.009975244120720287
chr15 102531392 240 2.340746529609195E-6 0.0015299480548420195
chr16 90354753 488 5.400933363184558E-6 0.002759420495882611
chr17 81195210 1011 1.2451473430513944E-5 0.008920398330804337
chr18 78077248 324 4.149736425136296E-6 0.002725531823151837
chr19 59128983 136 2.3000564714600282E-6 0.0015165919626584656
chr20 63025520 351 5.569172614521864E-6 0.002999387395158605
chr21 48129895 3116 6.474146681599867E-5 0.028652791004448123
chr22 51304566 30 5.847432760663057E-7 7.646848593646972E-4
chrMT 16571 2172091 131.07784684086658 715.036372034532
chrX 155270560 15369 9.898206073321305E-5 0.028870901420082647
chrY 59373566 228 3.840092744303079E-6 0.00307660153711105