BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6063547.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 = 1,722,585
number of mapped reads = 1,536,734 (89.21%)
number of supplementary alignments = 12,567 (0.73%)
number of secondary alignments = 0
number of mapped bases = 99,405,329 bp
number of sequenced bases = 99,360,405 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 84,868
duplication rate = 4.4%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.3728
>>>>>>> ACTG content
number of A's = 26,693,880 bp (26.87%)
number of C's = 17,704,461 bp (17.82%)
number of T's = 32,192,639 bp (32.4%)
number of G's = 22,766,895 bp (22.91%)
number of N's = 2,530 bp (0%)
GC percentage = 40.73%
>>>>>>> Mismatches and indels
general error rate = 0.0083
number of mismatches = 814,539
number of insertions = 7,600
mapped reads with insertion percentage = 0.49%
number of deletions = 27,784
mapped reads with deletion percentage = 1.79%
homopolymer indels = 46.36%
>>>>>>> Coverage
mean coverageData = 0.0321X
std coverageData = 0.3614X
There is a 2.67% of reference with a coverageData >= 1X
There is a 0.39% 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% 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 12184243 0.04888350107661316 0.7322259604467949
chr2 243199373 10298342 0.04234526542138741 0.4771005102160765
chr3 198022430 8111237 0.04096120323339129 0.23860336236160748
chr4 191154276 4807304 0.025148817492317045 0.18981860580048754
chr5 180915260 3011068 0.016643526919730266 0.15074609868652042
chr6 171115067 6985634 0.04082418995867851 0.28745640342938705
chr7 159138663 7182785 0.04513538611292719 0.5924216328004754
chr8 146364022 3697846 0.025264719768359468 0.42581765770147056
chr9 141213431 3075513 0.02177918189665684 0.2624714804751413
chr10 135534747 4131807 0.030485223099283906 0.3015900154296935
chr11 135006516 3808119 0.028206927434524715 0.24308712728663454
chr12 133851895 3760629 0.028095448331157357 0.2008267456239242
chr13 115169878 2245530 0.01949754605106033 0.16568844995246917
chr14 107349540 2640836 0.024600347612109004 0.19411623261919575
chr15 102531392 2051372 0.020007257874739476 0.17611164454141573
chr16 90354753 1975564 0.021864527702267086 0.18122730932674636
chr17 81195210 2648820 0.03262286038794653 0.22389776092962782
chr18 78077248 2308103 0.029561787321192468 0.40621664623026865
chr19 59128983 2636057 0.04458147030873168 0.44635129944687385
chr20 63025520 1369679 0.021732133269190004 0.1818414873490731
chr21 48129895 1508290 0.03133790339663114 0.20996088499388796
chr22 51304566 1230660 0.023987338670791992 0.17768553780583693
chrMT 16571 19715 1.1897290447166737 1.3451052567064532
chrX 155270560 7456923 0.04802535007280195 0.278424817131282
chrY 59373566 259253 0.00436647177297722 0.10723444643926222