BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525169.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 = 943,881
number of mapped reads = 867,463 (91.9%)
number of supplementary alignments = 3,074 (0.33%)
number of secondary alignments = 0
number of mapped bases = 51,962,353 bp
number of sequenced bases = 51,945,829 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 19,284
duplication rate = 1.59%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.4074
>>>>>>> ACTG content
number of A's = 13,256,852 bp (25.52%)
number of C's = 9,932,621 bp (19.12%)
number of T's = 16,293,647 bp (31.37%)
number of G's = 12,461,418 bp (23.99%)
number of N's = 1,291 bp (0%)
GC percentage = 43.11%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 256,410
number of insertions = 2,946
mapped reads with insertion percentage = 0.34%
number of deletions = 10,340
mapped reads with deletion percentage = 1.18%
homopolymer indels = 43.75%
>>>>>>> Coverage
mean coverageData = 0.0168X
std coverageData = 0.1845X
There is a 1.57% of reference with a coverageData >= 1X
There is a 0.07% 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 5460111 0.02190610790895482 0.3173196159568712
chr2 243199373 4210796 0.017314172927575762 0.206860514708086
chr3 198022430 3177921 0.016048288065144942 0.13434572024718633
chr4 191154276 2790873 0.014600107611508518 0.1288327003039523
chr5 180915260 2274473 0.012572035106380745 0.11696353322728223
chr6 171115067 3105819 0.01815047064207385 0.14773700586585223
chr7 159138663 3812569 0.02395752815894903 0.31272129527303466
chr8 146364022 3357475 0.022939209746504506 0.18151536904488663
chr9 141213431 1700792 0.012044123480010906 0.1390781784036012
chr10 135534747 3497531 0.025805419476674862 0.20626756203842567
chr11 135006516 2343862 0.017361102778179982 0.16437637890293777
chr12 133851895 2257060 0.01686236866500844 0.1363987764744006
chr13 115169878 1553072 0.013485053791582553 0.12199043514157407
chr14 107349540 1155606 0.010764890096408424 0.11329555900867118
chr15 102531392 1426133 0.01390923279379646 0.12378014719342417
chr16 90354753 1391459 0.015399953558613568 0.13892923815603134
chr17 81195210 926723 0.011413518112706402 0.11481436339428497
chr18 78077248 1096377 0.014042208557350793 0.2516249803011096
chr19 59128983 1023409 0.017308077157356147 0.22614792940112166
chr20 63025520 962539 0.01527221036811755 0.1301732514086351
chr21 48129895 702850 0.01460318997163821 0.1308411806358431
chr22 51304566 752361 0.01466460119748406 0.12615272246546397
chrMT 16571 5109 0.30830969766459476 0.5478627812668373
chrX 155270560 2834438 0.018254832081496968 0.14840944382798377
chrY 59373566 142995 0.002408395008647451 0.07045396060218737