BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1549139.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 = 13,247,905
number of mapped reads = 11,524,497 (86.99%)
number of secondary alignments = 0
number of mapped bases = 457,475,205 bp
number of sequenced bases = 457,426,547 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 652,378
duplication rate = 4.4%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 43.8582
>>>>>>> ACTG content
number of A's = 133,129,335 bp (29.1%)
number of C's = 94,950,368 bp (20.76%)
number of T's = 134,361,209 bp (29.37%)
number of G's = 94,884,997 bp (20.74%)
number of N's = 100,638 bp (0.02%)
GC percentage = 41.5%
>>>>>>> Mismatches and indels
general error rate = 0.0033
number of mismatches = 1,501,930
number of insertions = 11,319
mapped reads with insertion percentage = 0.1%
number of deletions = 37,995
mapped reads with deletion percentage = 0.33%
homopolymer indels = 44.99%
>>>>>>> Coverage
mean coverageData = 0.1478X
std coverageData = 1.0051X
There is a 10.17% of reference with a coverageData >= 1X
There is a 2.98% of reference with a coverageData >= 2X
There is a 0.92% of reference with a coverageData >= 3X
There is a 0.3% of reference with a coverageData >= 4X
There is a 0.11% 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 0.01% of reference with a coverageData >= 13X
There is a 0.01% 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 37488517 0.15040490912157045 1.7381545132900296
chr2 243199373 39489162 0.16237361763264085 0.8538228298072807
chr3 198022430 31553504 0.15934308047830742 0.537877563754063
chr4 191154276 29888112 0.15635596872549165 0.6776776603058511
chr5 180915260 28699843 0.15863693864188128 0.5525835511666662
chr6 171115067 26900454 0.15720681101682296 0.5916912904121224
chr7 159138663 25818908 0.16224157921950116 1.2473248883123784
chr8 146364022 23723031 0.16208239344502298 2.354882601953775
chr9 141213431 19521557 0.13824150338787533 0.7222382698680221
chr10 135534747 22149846 0.16342559004444815 0.9626734684685492
chr11 135006516 21305696 0.15781235329411805 0.7339703489862538
chr12 133851895 20997188 0.15686881384832094 0.5567502594610313
chr13 115169878 14747528 0.12805021813082063 0.47965544640907604
chr14 107349540 14053652 0.1309148786291958 0.6272902486075312
chr15 102531392 13670351 0.1333284444241233 0.48770341600421374
chr16 90354753 13301843 0.14721796649701427 0.5896745232219494
chr17 81195210 12483804 0.15375049833604718 0.5869187470923755
chr18 78077248 12196783 0.15621430458204674 1.4189198108516985
chr19 59128983 9130926 0.15442386350531345 1.4158463357445765
chr20 63025520 9789725 0.15532953952621098 0.597371226429157
chr21 48129895 6058889 0.12588618778412045 0.6502756422343161
chr22 51304566 5414113 0.10552887242043915 0.4728790834736678
chrMT 16571 201562 12.163538712208075 14.399289179259602
chrX 155270560 14891229 0.09590503827641247 0.5227679253739888
chrY 59373566 3998982 0.06735290246841498 0.7315117868707335