BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716992.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 = 2,474,368
number of mapped reads = 2,231,887 (90.2%)
number of supplementary alignments = 8,556 (0.35%)
number of secondary alignments = 0
number of mapped bases = 129,104,928 bp
number of sequenced bases = 129,065,543 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 91,330
duplication rate = 3.04%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.2959
>>>>>>> ACTG content
number of A's = 30,749,607 bp (23.82%)
number of C's = 25,774,979 bp (19.97%)
number of T's = 39,769,889 bp (30.81%)
number of G's = 32,770,027 bp (25.39%)
number of N's = 1,041 bp (0%)
GC percentage = 45.36%
>>>>>>> Mismatches and indels
general error rate = 0.0054
number of mismatches = 677,797
number of insertions = 7,230
mapped reads with insertion percentage = 0.32%
number of deletions = 24,405
mapped reads with deletion percentage = 1.09%
homopolymer indels = 42.08%
>>>>>>> Coverage
mean coverageData = 0.0417X
std coverageData = 0.3264X
There is a 3.6% of reference with a coverageData >= 1X
There is a 0.42% of reference with a coverageData >= 2X
There is a 0.07% of reference with a coverageData >= 3X
There is a 0.02% 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 10353547 0.0415387009206288 0.422243445177913
chr2 243199373 10843120 0.04458531231492936 0.5094755912404021
chr3 198022430 8592757 0.043392846961831544 0.24069092167959724
chr4 191154276 8216052 0.04298126189968149 0.2711962457764852
chr5 180915260 7661326 0.042347594116715195 0.23328228190663242
chr6 171115067 7359708 0.04301028617193599 0.2792532997455291
chr7 159138663 7115424 0.044712101169280274 0.4181984961812256
chr8 146364022 6392947 0.043678404792675075 0.3179483864932964
chr9 141213431 5444888 0.03855786210590691 0.2877840542962738
chr10 135534747 6275895 0.04630469410180107 0.4169282064667685
chr11 135006516 5815284 0.04307409873461219 0.3003180722727314
chr12 133851895 5839269 0.04362485118346662 0.24069680145862707
chr13 115169878 3985944 0.03460925781305421 0.20981428579874564
chr14 107349540 3871713 0.03606641444388117 0.2268036578361777
chr15 102531392 3798945 0.03705153052052585 0.22054489780003442
chr16 90354753 3874408 0.0428799578479286 0.2588235393310202
chr17 81195210 3733393 0.045980458699472544 0.2583821213449361
chr18 78077248 3345208 0.04284485026931277 0.46710299648099396
chr19 59128983 2858728 0.048347322327529293 0.37806570380540616
chr20 63025520 2847688 0.04518309408633201 0.25367676533016614
chr21 48129895 1695888 0.03523564720014453 0.2521984609207127
chr22 51304566 1589576 0.03098312925987913 0.20119061933329901
chrMT 16571 23964 1.446140848470219 1.5399699486562435
chrX 155270560 7162085 0.04612648399026834 0.26864382376448354
chrY 59373566 407171 0.006857782468379952 0.20834287423124084