BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524413.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 = 548,571
number of mapped reads = 503,870 (91.85%)
number of supplementary alignments = 1,798 (0.33%)
number of secondary alignments = 0
number of mapped bases = 29,188,700 bp
number of sequenced bases = 29,180,195 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 10,266
duplication rate = 1.52%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.6405
>>>>>>> ACTG content
number of A's = 6,950,375 bp (23.82%)
number of C's = 5,628,039 bp (19.29%)
number of T's = 9,678,054 bp (33.17%)
number of G's = 6,920,334 bp (23.72%)
number of N's = 3,393 bp (0.01%)
GC percentage = 43%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 144,073
number of insertions = 2,290
mapped reads with insertion percentage = 0.45%
number of deletions = 5,370
mapped reads with deletion percentage = 1.05%
homopolymer indels = 41.42%
>>>>>>> Coverage
mean coverageData = 0.0094X
std coverageData = 0.1247X
There is a 0.9% of reference with a coverageData >= 1X
There is a 0.03% 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 2340097 0.009388530269699909 0.21563974441324235
chr2 243199373 2341064 0.00962611034363152 0.13371348445403416
chr3 198022430 1981325 0.010005558461230881 0.10297039388101308
chr4 191154276 1951637 0.01020974806757658 0.11008777383445092
chr5 180915260 1784887 0.009865873116507695 0.10246344755877232
chr6 171115067 1069698 0.006251337294570326 0.0842738775084642
chr7 159138663 1649489 0.010365105304422471 0.15979498816325588
chr8 146364022 2179725 0.014892491817422181 0.14281967394043402
chr9 141213431 1084139 0.0076773079750466515 0.09977482764212815
chr10 135534747 1448472 0.010687089709917708 0.12099578841271282
chr11 135006516 1196061 0.008859283503027365 0.10808296332643241
chr12 133851895 1250035 0.009338941372477394 0.10090313744534386
chr13 115169878 845717 0.007343213474620508 0.0885808453663075
chr14 107349540 809379 0.007539659694862223 0.09033102899082479
chr15 102531392 857436 0.00836266808900829 0.09433047833832882
chr16 90354753 874215 0.009675362623148337 0.10355887464581912
chr17 81195210 748200 0.009214829298427827 0.10107573505733182
chr18 78077248 793890 0.010168006946146462 0.14360292953838086
chr19 59128983 803818 0.013594314652765125 0.15945475120211383
chr20 63025520 812895 0.012897870576871083 0.11844602127035261
chr21 48129895 377275 0.007838683213416527 0.09482412940349744
chr22 51304566 195367 0.003807984653841531 0.0634967186722163
chrMT 16571 9908 0.5979120149659043 0.8284034970074621
chrX 155270560 1698959 0.01094192614491762 0.11256681577225701
chrY 59373566 85012 0.0014318156332398832 0.05111163510816557