BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1549136.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 13,649,303
number of mapped reads = 12,038,981 (88.2%)
number of secondary alignments = 0
number of mapped bases = 477,617,136 bp
number of sequenced bases = 477,569,137 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 637,735
duplication rate = 4.08%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.4047
>>>>>>> ACTG content
number of A's = 133,973,618 bp (28.05%)
number of C's = 104,236,924 bp (21.83%)
number of T's = 135,483,798 bp (28.37%)
number of G's = 103,774,208 bp (21.73%)
number of N's = 100,589 bp (0.02%)
GC percentage = 43.56%
>>>>>>> Mismatches and indels
general error rate = 0.0033
number of mismatches = 1,556,675
number of insertions = 13,154
mapped reads with insertion percentage = 0.11%
number of deletions = 38,049
mapped reads with deletion percentage = 0.32%
homopolymer indels = 46.34%
>>>>>>> Coverage
mean coverageData = 0.1543X
std coverageData = 0.9196X
There is a 10.92% of reference with a coverageData >= 1X
There is a 2.94% of reference with a coverageData >= 2X
There is a 0.88% of reference with a coverageData >= 3X
There is a 0.29% of reference with a coverageData >= 4X
There is a 0.1% of reference with a coverageData >= 5X
There is a 0.04% of reference with a coverageData >= 6X
There is a 0.02% 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% 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 39959757 0.1603195885317373 1.618751796824112
chr2 243199373 40007526 0.164505054048803 0.9115607697988309
chr3 198022430 31537382 0.15926166545880685 0.5411618410209975
chr4 191154276 28246806 0.14776967897908808 0.5380339502593543
chr5 180915260 28436887 0.15718346257800475 0.5496899796052171
chr6 171115067 26698984 0.15602941615889382 0.6159058363261191
chr7 159138663 27451101 0.17249799943336208 1.5244924695090103
chr8 146364022 24122731 0.1648132558150117 1.0854310834660348
chr9 141213431 20728855 0.146790959282053 0.8622504406072301
chr10 135534747 23291577 0.1718494888989611 0.8164237865691742
chr11 135006516 22219879 0.16458375238718106 0.7727208757943662
chr12 133851895 21878445 0.16345263546698385 0.5810578474476349
chr13 115169878 14122797 0.12262578762130841 0.4523442946465441
chr14 107349540 14956466 0.13932491932429333 0.6946535310849863
chr15 102531392 14971286 0.14601660728452803 0.5039829389440822
chr16 90354753 15621271 0.17288820434272006 0.6229457201175759
chr17 81195210 15609186 0.19224269510479744 0.6270139455161855
chr18 78077248 12438383 0.15930867594103726 1.7811553000405402
chr19 59128983 12144817 0.20539533040843946 1.4775255297296683
chr20 63025520 11380218 0.1805652377005378 0.6178168038466374
chr21 48129895 6397390 0.13291925943324828 0.6150323231936329
chr22 51304566 7244789 0.14121138847563783 0.5762114215186032
chrMT 16571 10368 0.6256713535694889 1.2587761893170668
chrX 155270560 14820999 0.09545273102640964 0.5744782643152462
chrY 59373566 3319236 0.05590427228170867 0.3838325222205196