BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525046.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 = 1,239,867
number of mapped reads = 1,141,629 (92.08%)
number of supplementary alignments = 3,471 (0.28%)
number of secondary alignments = 0
number of mapped bases = 66,925,436 bp
number of sequenced bases = 66,903,636 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 61,103
duplication rate = 4.37%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.2804
>>>>>>> ACTG content
number of A's = 17,517,251 bp (26.18%)
number of C's = 12,298,344 bp (18.38%)
number of T's = 20,579,628 bp (30.76%)
number of G's = 16,501,663 bp (24.66%)
number of N's = 6,750 bp (0.01%)
GC percentage = 43.05%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 323,956
number of insertions = 4,421
mapped reads with insertion percentage = 0.39%
number of deletions = 13,528
mapped reads with deletion percentage = 1.18%
homopolymer indels = 43.76%
>>>>>>> Coverage
mean coverageData = 0.0216X
std coverageData = 0.2287X
There is a 1.92% of reference with a coverageData >= 1X
There is a 0.18% of reference with a coverageData >= 2X
There is a 0.02% of reference with a coverageData >= 3X
There is a 0.01% 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 5360391 0.021506028665019855 0.4087381057257579
chr2 243199373 5507387 0.022645564139673995 0.2741441262657525
chr3 198022430 4230859 0.02136555439704482 0.1607763844143997
chr4 191154276 4469885 0.02338365164271816 0.18656158592912236
chr5 180915260 4470552 0.024710751320811745 0.172787603272139
chr6 171115067 3695735 0.0215979519792959 0.17306257008060472
chr7 159138663 3664032 0.023024147186658215 0.27670336138364027
chr8 146364022 3324566 0.022714366239539385 0.2674482585305381
chr9 141213431 2776511 0.019661805398666365 0.18380080783287056
chr10 135534747 3622217 0.026725375449293456 0.25765724909237075
chr11 135006516 2982683 0.022092881798386678 0.18609884474627353
chr12 133851895 2869191 0.02143556503253092 0.16474695877944417
chr13 115169878 2044287 0.01775018811776461 0.1467876067756215
chr14 107349540 1918529 0.017871795258740747 0.1511818240548303
chr15 102531392 1831088 0.017858803672537674 0.14705111925159417
chr16 90354753 1848229 0.020455249321527116 0.16774146281638866
chr17 81195210 2048116 0.025224591450653307 0.1838042680237242
chr18 78077248 1754536 0.022471796137076963 0.28683636709708676
chr19 59128983 1369402 0.023159573030369893 0.3029688211714736
chr20 63025520 1470792 0.023336451646888436 0.17357231326261202
chr21 48129895 944926 0.019632829034844146 0.17096426303003587
chr22 51304566 863205 0.016825110653893846 0.14222899249320572
chrMT 16571 6733 0.4063122322129021 0.701950882209028
chrX 155270560 3625470 0.023349371574366704 0.18234385660620916
chrY 59373566 226114 0.003808327766602397 0.14012997482528552