BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716312.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 = 2,322,786
number of mapped reads = 2,181,624 (93.92%)
number of supplementary alignments = 40,956 (1.76%)
number of secondary alignments = 0
number of mapped bases = 172,940,998 bp
number of sequenced bases = 172,863,192 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 103,908
duplication rate = 3.46%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 47.5589
>>>>>>> ACTG content
number of A's = 45,264,774 bp (26.19%)
number of C's = 34,503,822 bp (19.96%)
number of T's = 52,509,721 bp (30.38%)
number of G's = 40,572,882 bp (23.47%)
number of N's = 11,993 bp (0.01%)
GC percentage = 43.43%
>>>>>>> Mismatches and indels
general error rate = 0.0066
number of mismatches = 1,106,471
number of insertions = 15,600
mapped reads with insertion percentage = 0.71%
number of deletions = 41,193
mapped reads with deletion percentage = 1.86%
homopolymer indels = 41.91%
>>>>>>> Coverage
mean coverageData = 0.0559X
std coverageData = 0.5024X
There is a 4.62% of reference with a coverageData >= 1X
There is a 0.67% of reference with a coverageData >= 2X
There is a 0.13% of reference with a coverageData >= 3X
There is a 0.04% of reference with a coverageData >= 4X
There is a 0.02% of reference with a coverageData >= 5X
There is a 0.01% of reference with a coverageData >= 6X
There is a 0.01% 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 16703704 0.06701569662287822 1.050091685433791
chr2 243199373 14189953 0.058346996642955985 0.557252391201184
chr3 198022430 10972626 0.0554110259125696 0.2707268309313777
chr4 191154276 10954691 0.057308113787629844 0.33756540189015966
chr5 180915260 10061144 0.05561246740601097 0.2741952317855109
chr6 171115067 9616875 0.05620121692732061 0.3030953309693159
chr7 159138663 9059694 0.05692955960048502 0.6124638449995515
chr8 146364022 8527053 0.058259214822615354 0.5702980343011433
chr9 141213431 7051316 0.04993374886557356 0.41193525886389637
chr10 135534747 7981652 0.05889007930933018 0.47036674239920795
chr11 135006516 9613202 0.07120546685317025 0.5591008304346482
chr12 133851895 7589949 0.05670408327054316 0.2788225371825856
chr13 115169878 6037590 0.052423342846642594 0.26745036357403945
chr14 107349540 4889594 0.0455483460851346 0.27779695524139864
chr15 102531392 4996564 0.04873204101237599 0.2549891327035384
chr16 90354753 3839904 0.04249808529718409 0.2712418488656035
chr17 81195210 5149612 0.06342260830411055 0.36278263440439146
chr18 78077248 4553027 0.058314388847311834 0.7321915682521372
chr19 59128983 3298496 0.05578475787415454 0.7536754032449012
chr20 63025520 3599140 0.057106073857066154 0.29072131992324407
chr21 48129895 2256604 0.04688570378140239 0.28725879930785786
chr22 51304566 1926503 0.0375503225190522 0.227026101653551
chrMT 16571 39790 2.4011827892100657 2.295027311774326
chrX 155270560 9534804 0.06140767444903915 0.3508844883702781
chrY 59373566 497511 0.008379335005749866 0.2594352862728055