BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525248.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 = 1,444,781
number of mapped reads = 1,333,241 (92.28%)
number of supplementary alignments = 5,189 (0.36%)
number of secondary alignments = 0
number of mapped bases = 77,764,791 bp
number of sequenced bases = 77,741,527 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 38,471
duplication rate = 1.99%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.4553
>>>>>>> ACTG content
number of A's = 19,901,109 bp (25.6%)
number of C's = 13,830,701 bp (17.79%)
number of T's = 24,493,095 bp (31.51%)
number of G's = 19,515,230 bp (25.1%)
number of N's = 1,392 bp (0%)
GC percentage = 42.89%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 383,446
number of insertions = 6,222
mapped reads with insertion percentage = 0.46%
number of deletions = 14,627
mapped reads with deletion percentage = 1.09%
homopolymer indels = 40.74%
>>>>>>> Coverage
mean coverageData = 0.0251X
std coverageData = 0.2406X
There is a 2.31% of reference with a coverageData >= 1X
There is a 0.14% 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 6448702 0.025872360815502243 0.3822274669876213
chr2 243199373 6183972 0.025427582002853274 0.2953109818273515
chr3 198022430 4472330 0.022584966763613597 0.1626660555021932
chr4 191154276 4857151 0.025409585920013633 0.18757845097979134
chr5 180915260 4500884 0.024878409925177123 0.1670872236520788
chr6 171115067 4152681 0.02426835387908886 0.19774642232735504
chr7 159138663 4420516 0.027777762591859906 0.34133803022721243
chr8 146364022 4092568 0.027961571047835785 0.3012437830342122
chr9 141213431 2570025 0.018199579047123358 0.17688654725822084
chr10 135534747 3452285 0.02547158626414819 0.2656168808238492
chr11 135006516 2781918 0.020605805426458082 0.18854700635512178
chr12 133851895 3831964 0.028628388115087947 0.18197660662703444
chr13 115169878 2572669 0.022338037034301626 0.15993797544129945
chr14 107349540 2587864 0.024106894170203244 0.16792901732508714
chr15 102531392 2816349 0.027468163116326362 0.17763469442788074
chr16 90354753 2595105 0.02872128929398988 0.1937348370335593
chr17 81195210 3318574 0.040871548949747157 0.22511855751077872
chr18 78077248 1473833 0.018876600261320684 0.29896184002144904
chr19 59128983 1890886 0.031979004272743874 0.3254768971229625
chr20 63025520 2512499 0.039864788104881956 0.2193406778760054
chr21 48129895 989361 0.020556059804410543 0.17231355378062146
chr22 51304566 679486 0.013244162322706325 0.12263635189935372
chrMT 16571 4090 0.24681672801882806 0.5226462553442752
chrX 155270560 4291554 0.02763919960100614 0.1897427915744182
chrY 59373566 267525 0.004505793032542462 0.18024295808223606