BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524400.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 = 377,706
number of mapped reads = 332,598 (88.06%)
number of supplementary alignments = 1,104 (0.29%)
number of secondary alignments = 0
number of mapped bases = 19,080,183 bp
number of sequenced bases = 19,073,833 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 5,736
duplication rate = 1.33%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.3967
>>>>>>> ACTG content
number of A's = 4,749,853 bp (24.9%)
number of C's = 3,254,712 bp (17.06%)
number of T's = 6,442,109 bp (33.77%)
number of G's = 4,626,754 bp (24.26%)
number of N's = 405 bp (0%)
GC percentage = 41.32%
>>>>>>> Mismatches and indels
general error rate = 0.0053
number of mismatches = 98,956
number of insertions = 1,301
mapped reads with insertion percentage = 0.39%
number of deletions = 4,052
mapped reads with deletion percentage = 1.21%
homopolymer indels = 44.39%
>>>>>>> Coverage
mean coverageData = 0.0062X
std coverageData = 0.093X
There is a 0.59% of reference with a coverageData >= 1X
There is a 0.02% 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 1502676 0.006028775350573751 0.12912893330848896
chr2 243199373 1647574 0.006774581610455056 0.1169867224323617
chr3 198022430 1297597 0.006552777884808301 0.0829906866141489
chr4 191154276 1246956 0.00652329639751297 0.08421353054709071
chr5 180915260 1174313 0.006490956042071852 0.08274306003961245
chr6 171115067 1121617 0.006554753007226418 0.08605706701204141
chr7 159138663 1052456 0.006613452571233428 0.11000855590808419
chr8 146364022 965622 0.006597400008589543 0.09826288988877123
chr9 141213431 786326 0.00556835135604063 0.08090114583130953
chr10 135534747 916012 0.006758503042765852 0.09269163716642317
chr11 135006516 867720 0.006427245333847442 0.08600801722542827
chr12 133851895 862973 0.006447222880184102 0.08243612752878299
chr13 115169878 599387 0.005204372969814208 0.07411979181720445
chr14 107349540 574327 0.0053500648442461884 0.07517068355928741
chr15 102531392 523793 0.005108611029098288 0.07308877798427736
chr16 90354753 543513 0.006015322735706001 0.08170867003459518
chr17 81195210 506559 0.006238779356565492 0.08144549408894461
chr18 78077248 505414 0.006473255819672332 0.10773901845778928
chr19 59128983 372027 0.006291787565498971 0.1039203595841937
chr20 63025520 396134 0.0062852952264416066 0.08150561326488967
chr21 48129895 247131 0.0051346673413686025 0.07403762711367358
chr22 51304566 210821 0.004109205406785821 0.06585698845536522
chrMT 16571 10140 0.611912377044234 0.885187706645735
chrX 155270560 1084117 0.006982115605173318 0.08776071216633273
chrY 59373566 64978 0.0010943927471023047 0.04399421045029051