BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6237267.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,030,819
number of mapped reads = 1,820,900 (89.66%)
number of supplementary alignments = 11,720 (0.58%)
number of secondary alignments = 0
number of mapped bases = 122,164,696 bp
number of sequenced bases = 122,102,318 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 97,264
duplication rate = 4.15%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.1682
>>>>>>> ACTG content
number of A's = 34,654,062 bp (28.38%)
number of C's = 21,832,058 bp (17.88%)
number of T's = 39,450,800 bp (32.31%)
number of G's = 26,163,424 bp (21.43%)
number of N's = 1,974 bp (0%)
GC percentage = 39.31%
>>>>>>> Mismatches and indels
general error rate = 0.0079
number of mismatches = 946,497
number of insertions = 9,715
mapped reads with insertion percentage = 0.53%
number of deletions = 35,487
mapped reads with deletion percentage = 1.93%
homopolymer indels = 46.52%
>>>>>>> Coverage
mean coverageData = 0.0395X
std coverageData = 0.4097X
There is a 3.16% of reference with a coverageData >= 1X
There is a 0.56% of reference with a coverageData >= 2X
There is a 0.11% of reference with a coverageData >= 3X
There is a 0.03% 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% 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 12268165 0.049220198332023415 0.6314737003882563
chr2 243199373 6775396 0.027859430377725522 0.34317253900911887
chr3 198022430 12079131 0.0609988020043992 0.29482683861119585
chr4 191154276 6507038 0.03404076610873199 0.24698732526749967
chr5 180915260 6415674 0.035462315340342214 0.22587883953726706
chr6 171115067 16410184 0.09590145559771192 0.7007519114284116
chr7 159138663 6280114 0.0394631567314349 0.38659085840624996
chr8 146364022 8441775 0.05767657163725659 0.7960966528829447
chr9 141213431 5857995 0.04148327080870941 0.36990342930675
chr10 135534747 1634623 0.01206054562524841 0.2992787007338923
chr11 135006516 9117277 0.0675321256345879 0.4303433942907592
chr12 133851895 3628536 0.027108588937048667 0.20612429550764838
chr13 115169878 5182883 0.045002070767149724 0.253509077775474
chr14 107349540 3837043 0.03574345078702713 0.24597682502196294
chr15 102531392 2011356 0.0196169774033693 0.1722256706825591
chr16 90354753 1741128 0.019269910460604105 0.21245254470375285
chr17 81195210 570737 0.0070291954414552285 0.143664668299523
chr18 78077248 2087834 0.02674061975135189 0.6809699928917669
chr19 59128983 1048781 0.017737172986722942 0.36527689276101316
chr20 63025520 1873888 0.029732210063479047 0.21255743839823607
chr21 48129895 2289747 0.047574319453636875 0.28769811849390886
chr22 51304566 706078 0.0137624787626115 0.1372801230509183
chrMT 16571 252429 15.233178444270111 8.972134417857799
chrX 155270560 4821368 0.031051398281812085 0.22837742124821162
chrY 59373566 325516 0.005482507148046321 0.15894158612097722