BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1548981.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 = 10,224,172
number of mapped reads = 4,435,479 (43.38%)
number of secondary alignments = 0
number of mapped bases = 175,037,913 bp
number of sequenced bases = 175,015,442 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 122,878
duplication rate = 2.14%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.8741
>>>>>>> ACTG content
number of A's = 52,929,627 bp (30.24%)
number of C's = 34,455,266 bp (19.69%)
number of T's = 53,171,939 bp (30.38%)
number of G's = 34,449,348 bp (19.68%)
number of N's = 9,262 bp (0.01%)
GC percentage = 39.37%
>>>>>>> Mismatches and indels
general error rate = 0.0031
number of mismatches = 536,514
number of insertions = 7,695
mapped reads with insertion percentage = 0.17%
number of deletions = 18,162
mapped reads with deletion percentage = 0.41%
homopolymer indels = 45.25%
>>>>>>> Coverage
mean coverageData = 0.0565X
std coverageData = 0.3849X
There is a 4.66% of reference with a coverageData >= 1X
There is a 0.75% of reference with a coverageData >= 2X
There is a 0.14% 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 13920888 0.05585096616469413 0.6284750891577553
chr2 243199373 15342069 0.0630843279353356 0.3574370603784929
chr3 198022430 12583905 0.06354787687435207 0.296270635441695
chr4 191154276 12385249 0.06479190138545475 0.3035346600441524
chr5 180915260 11308026 0.06250454494551759 0.2950922037580907
chr6 171115067 10700938 0.0625365035797812 0.32993729966920976
chr7 159138663 10046049 0.06312764485145889 0.5666035454797432
chr8 146364022 9291009 0.06347877622548526 0.6347066774738255
chr9 141213431 7447984 0.052742745128825604 0.31790402426535447
chr10 135534747 8052115 0.05940996813164081 0.318345642895511
chr11 135006516 8113958 0.06010049174219117 0.3319904582090719
chr12 133851895 8015663 0.059884568686905774 0.2933369811115016
chr13 115169878 6090700 0.052884487730376864 0.27038242268207024
chr14 107349540 5651130 0.05264233083812003 0.29346924132882485
chr15 102531392 4968257 0.04845595971231913 0.25832289045081286
chr16 90354753 4613108 0.05105551005158522 0.27057999115045417
chr17 81195210 4254436 0.052397622963226524 0.2760788866944253
chr18 78077248 4828954 0.06184841453428277 0.46815495236803123
chr19 59128983 2889887 0.0488742889421927 0.5265071046039758
chr20 63025520 3405649 0.05403603175348652 0.2784434332400896
chr21 48129895 2210162 0.045920773357182684 0.26706572086376035
chr22 51304566 1737335 0.03386316531748851 0.2720800486583692
chrMT 16571 6249 0.3771045802908696 0.7091934662022161
chrX 155270560 5929334 0.03818711029315538 0.2518735708642066
chrY 59373566 1244859 0.02096655269114205 0.1942679598346313