BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525224.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 1,018,124
number of mapped reads = 956,606 (93.96%)
number of supplementary alignments = 4,216 (0.41%)
number of secondary alignments = 0
number of mapped bases = 60,207,054 bp
number of sequenced bases = 60,184,242 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 19,729
duplication rate = 1.4%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.7549
>>>>>>> ACTG content
number of A's = 15,785,267 bp (26.23%)
number of C's = 13,067,865 bp (21.71%)
number of T's = 18,068,693 bp (30.02%)
number of G's = 13,260,980 bp (22.03%)
number of N's = 1,437 bp (0%)
GC percentage = 43.75%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 293,026
number of insertions = 4,774
mapped reads with insertion percentage = 0.5%
number of deletions = 13,721
mapped reads with deletion percentage = 1.42%
homopolymer indels = 42.21%
>>>>>>> Coverage
mean coverageData = 0.0194X
std coverageData = 0.2053X
There is a 1.8% of reference with a coverageData >= 1X
There is a 0.1% of reference with a coverageData >= 2X
There is a 0.01% 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 4894782 0.019637993198821358 0.37059520179405747
chr2 243199373 5019601 0.02063985995556 0.21065414969321514
chr3 198022430 3974780 0.020072372609506912 0.14974163708279264
chr4 191154276 3830835 0.020040540448072425 0.16310394816832915
chr5 180915260 3594553 0.019868710909184774 0.14809148802407573
chr6 171115067 3450886 0.020167049345806584 0.16059649089661054
chr7 159138663 3381090 0.021246188300576587 0.28428896495435807
chr8 146364022 3097114 0.021160350458256743 0.19041319925782413
chr9 141213431 2569961 0.018199125832442948 0.17837914951905404
chr10 135534747 2922135 0.021560043196893267 0.21920567319077097
chr11 135006516 2750249 0.020371231563371357 0.172498915796551
chr12 133851895 2706909 0.020223165312676372 0.1512816730800379
chr13 115169878 1888002 0.016393192671437927 0.1340216371592689
chr14 107349540 1854406 0.017274466197060554 0.1420761057680294
chr15 102531392 1684723 0.016431289648344966 0.13481606415716318
chr16 90354753 1780060 0.01970078984112767 0.1599033392133043
chr17 81195210 1614927 0.019889436827615816 0.15497390164893896
chr18 78077248 1603417 0.02053628990611964 0.3216313751124778
chr19 59128983 1240858 0.020985613772521675 0.2751868372040085
chr20 63025520 1250658 0.01984367602203044 0.15108420846899917
chr21 48129895 798847 0.016597729955571273 0.1479757400134603
chr22 51304566 712937 0.013896170566962792 0.1238451342444668
chrMT 16571 41103 2.480417597006819 1.9872601125351603
chrX 155270560 3347826 0.021561241229502877 0.16096023102767196
chrY 59373566 196395 0.0033077851513921195 0.11857239184043492