BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524720.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 = 234,783
number of mapped reads = 216,454 (92.19%)
number of supplementary alignments = 748 (0.32%)
number of secondary alignments = 0
number of mapped bases = 12,856,537 bp
number of sequenced bases = 12,852,539 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 2,654
duplication rate = 0.93%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.1126
>>>>>>> ACTG content
number of A's = 3,287,998 bp (25.58%)
number of C's = 2,402,971 bp (18.7%)
number of T's = 4,126,334 bp (32.11%)
number of G's = 3,033,228 bp (23.6%)
number of N's = 2,008 bp (0.02%)
GC percentage = 42.3%
>>>>>>> Mismatches and indels
general error rate = 0.0052
number of mismatches = 64,764
number of insertions = 931
mapped reads with insertion percentage = 0.43%
number of deletions = 2,484
mapped reads with deletion percentage = 1.14%
homopolymer indels = 44.54%
>>>>>>> Coverage
mean coverageData = 0.0042X
std coverageData = 0.0721X
There is a 0.4% of reference with a coverageData >= 1X
There is a 0.01% of reference with a coverageData >= 2X
There is a 0% 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 1043158 0.004185177135426274 0.09303843430551074
chr2 243199373 1087140 0.004470159550945881 0.08102036988437307
chr3 198022430 840325 0.004243584931262585 0.06631545191455115
chr4 191154276 843765 0.00441405244840037 0.06910304370798133
chr5 180915260 763207 0.004218588304822932 0.06618196111512349
chr6 171115067 749067 0.004377563081572472 0.06878087182508788
chr7 159138663 723439 0.0045459663061263745 0.07871606969345425
chr8 146364022 651462 0.004450970881354982 0.07663876684848582
chr9 141213431 535429 0.0037916294236912916 0.06662230565184316
chr10 135534747 630865 0.004654636644579415 0.07757258653293436
chr11 135006516 594578 0.004404068911755341 0.07087069085774111
chr12 133851895 572306 0.004275666026244903 0.06632992204638796
chr13 115169878 413866 0.0035935264253731344 0.06095013789994401
chr14 107349540 390727 0.0036397640828269968 0.06130435657280271
chr15 102531392 355273 0.0034650168408910317 0.05962157193197296
chr16 90354753 371351 0.004109922142114649 0.06646850943338074
chr17 81195210 340293 0.004191047723135392 0.06631680306082807
chr18 78077248 340821 0.004365176907874622 0.08549264227788662
chr19 59128983 255796 0.004326067979217569 0.08178085163119987
chr20 63025520 270250 0.0042879455814089276 0.06706286623903548
chr21 48129895 164259 0.003412826892724366 0.06116709320121183
chr22 51304566 146494 0.002855379382801913 0.05411444525412714
chrMT 16571 1713 0.10337336310421821 0.33411985397623645
chrX 155270560 724664 0.004667104955375958 0.07033528392024972
chrY 59373566 46289 7.796230396537072E-4 0.038410544280426735