BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524936.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 = 1,035,215
number of mapped reads = 952,434 (92%)
number of supplementary alignments = 3,895 (0.38%)
number of secondary alignments = 0
number of mapped bases = 55,715,950 bp
number of sequenced bases = 55,697,683 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 32,431
duplication rate = 2.64%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.0347
>>>>>>> ACTG content
number of A's = 14,318,282 bp (25.71%)
number of C's = 10,966,053 bp (19.69%)
number of T's = 17,397,223 bp (31.24%)
number of G's = 13,015,703 bp (23.37%)
number of N's = 422 bp (0%)
GC percentage = 43.06%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 282,319
number of insertions = 3,989
mapped reads with insertion percentage = 0.42%
number of deletions = 10,862
mapped reads with deletion percentage = 1.13%
homopolymer indels = 43.53%
>>>>>>> Coverage
mean coverageData = 0.018X
std coverageData = 0.189X
There is a 1.64% of reference with a coverageData >= 1X
There is a 0.11% of reference with a coverageData >= 2X
There is a 0.01% of reference with a coverageData >= 3X
There is a 0% 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 5841596 0.02343663569046835 0.33038798358732874
chr2 243199373 4821837 0.01982668351698423 0.21368757864166696
chr3 198022430 3458346 0.017464415521009413 0.14257286240766232
chr4 191154276 2555362 0.013368060885020433 0.14249183521617328
chr5 180915260 3382160 0.018694719284597663 0.14575287813138044
chr6 171115067 3547912 0.02073407130185678 0.16203595771434193
chr7 159138663 3296278 0.02071324427301491 0.2234046073856455
chr8 146364022 4962676 0.03390639265160396 0.24295654475819098
chr9 141213431 1998826 0.014154645105960212 0.15176175822673868
chr10 135534747 2408120 0.0177675470925548 0.20859376969550553
chr11 135006516 2772548 0.020536401368953183 0.1763936130192084
chr12 133851895 1777259 0.013277802305301692 0.12648662558350243
chr13 115169878 1570362 0.013635179851453866 0.12558330815355365
chr14 107349540 1034194 0.009633893168056426 0.10982522153665221
chr15 102531392 1420686 0.013856107600684871 0.1250732313540136
chr16 90354753 1633882 0.018082966814153098 0.1498016037947172
chr17 81195210 1277910 0.015738736312154375 0.13803977561665756
chr18 78077248 1481935 0.01898036928760604 0.236473713174765
chr19 59128983 1150856 0.01946348375381325 0.23859350625644335
chr20 63025520 1091722 0.017321903889091276 0.14554849382128968
chr21 48129895 501827 0.010426513500600821 0.12966971664307467
chr22 51304566 1024736 0.019973582858102728 0.1521391998861374
chrMT 16571 80111 4.834409510590791 3.2741828734461764
chrX 155270560 2465915 0.015881407267417595 0.14428588576135404
chrY 59373566 158894 0.002676174107514445 0.10884489121456811