BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6003988.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 3,353,811
number of mapped reads = 2,311,753 (68.93%)
number of supplementary alignments = 11,496 (0.34%)
number of secondary alignments = 0
number of mapped bases = 141,812,630 bp
number of sequenced bases = 141,740,457 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 447,380
duplication rate = 15.04%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.3077
>>>>>>> ACTG content
number of A's = 36,683,773 bp (25.88%)
number of C's = 23,078,342 bp (16.28%)
number of T's = 49,820,924 bp (35.15%)
number of G's = 32,143,263 bp (22.68%)
number of N's = 14,155 bp (0.01%)
GC percentage = 38.96%
>>>>>>> Mismatches and indels
general error rate = 0.0111
number of mismatches = 1,554,010
number of insertions = 12,274
mapped reads with insertion percentage = 0.53%
number of deletions = 44,684
mapped reads with deletion percentage = 1.91%
homopolymer indels = 48.92%
>>>>>>> Coverage
mean coverageData = 0.0458X
std coverageData = 0.4747X
There is a 2.48% of reference with a coverageData >= 1X
There is a 1.02% of reference with a coverageData >= 2X
There is a 0.5% of reference with a coverageData >= 3X
There is a 0.25% of reference with a coverageData >= 4X
There is a 0.13% of reference with a coverageData >= 5X
There is a 0.07% of reference with a coverageData >= 6X
There is a 0.03% of reference with a coverageData >= 7X
There is a 0.02% 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% 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 14321426 0.05745793507972845 0.6891610022809604
chr2 243199373 13288222 0.05463921159040159 0.7036983386535303
chr3 198022430 9438968 0.047666155798613316 0.36818127925877275
chr4 191154276 9465166 0.049515847607824376 0.383094739121294
chr5 180915260 7954655 0.0439689554103949 0.3525941880713993
chr6 171115067 9459029 0.055278761630032265 0.46059459169960537
chr7 159138663 7559622 0.04750336503706833 0.5101460204988777
chr8 146364022 8775339 0.05995557432823211 0.6249650664993912
chr9 141213431 5337860 0.03779994553067689 0.42782603639514505
chr10 135534747 5755405 0.04246442427047877 0.395443201243922
chr11 135006516 5353600 0.0396543823114434 0.3956160695760302
chr12 133851895 5926129 0.044273777371624065 0.35754699833661663
chr13 115169878 3151510 0.02736401266310276 0.2760160079480985
chr14 107349540 3406684 0.03173450021304237 0.3153013644455293
chr15 102531392 3548579 0.03460968324705862 0.312536524925011
chr16 90354753 4256393 0.04710757164042051 0.36664659521663856
chr17 81195210 3391875 0.04177432387945052 0.34241849545524056
chr18 78077248 3952433 0.05062208391361335 0.77830972272021
chr19 59128983 2281112 0.03857857660092006 0.4811551232736619
chr20 63025520 3282023 0.05207450886561507 0.38408477105962346
chr21 48129895 2336068 0.04853673584785506 0.3756320337071971
chr22 51304566 1484983 0.028944460810759028 0.26579704790320635
chrMT 16571 97553 5.886971214772796 7.552539858970981
chrX 155270560 7653917 0.049294064502633336 0.4143683043117493
chrY 59373566 334079 0.00562672957861416 0.11981059268008921