BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525145.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 = 1,046,228
number of mapped reads = 937,065 (89.57%)
number of supplementary alignments = 27,688 (2.65%)
number of secondary alignments = 0
number of mapped bases = 71,946,687 bp
number of sequenced bases = 71,918,416 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 22,813
duplication rate = 1.45%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.6821
>>>>>>> ACTG content
number of A's = 18,679,590 bp (25.97%)
number of C's = 14,405,816 bp (20.03%)
number of T's = 21,809,041 bp (30.32%)
number of G's = 17,021,331 bp (23.67%)
number of N's = 2,638 bp (0%)
GC percentage = 43.7%
>>>>>>> Mismatches and indels
general error rate = 0.0077
number of mismatches = 535,819
number of insertions = 7,070
mapped reads with insertion percentage = 0.75%
number of deletions = 16,409
mapped reads with deletion percentage = 1.73%
homopolymer indels = 41.24%
>>>>>>> Coverage
mean coverageData = 0.0232X
std coverageData = 0.2588X
There is a 2.12% 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 6920058 0.02776345339576907 0.41734772767061257
chr2 243199373 5977694 0.024579397250337483 0.3529812578352306
chr3 198022430 4590904 0.023183757516762115 0.1618565944411982
chr4 191154276 4542003 0.02376092805792113 0.17231920782694612
chr5 180915260 4225841 0.023358123576750794 0.1631102955738242
chr6 171115067 4023409 0.02351288563034604 0.1783910316822196
chr7 159138663 3869135 0.024312979178416246 0.368979993273501
chr8 146364022 3562669 0.024341152636540693 0.31541527950706344
chr9 141213431 2925362 0.020715890686063707 0.24580125248953025
chr10 135534747 3288291 0.024261608722374345 0.28028089647684507
chr11 135006516 3911058 0.02896940174354251 0.2786197978497338
chr12 133851895 3143610 0.023485733989795213 0.1632146349632041
chr13 115169878 2568867 0.022305024930216563 0.15980075784818903
chr14 107349540 2104918 0.019608076569308075 0.16722102039482123
chr15 102531392 1980983 0.01932074617693672 0.1474791727300062
chr16 90354753 1646179 0.018219063694413506 0.1575430618671818
chr17 81195210 2197482 0.027064182727035254 0.19896620678909813
chr18 78077248 1885460 0.02414864827202926 0.40781746381252487
chr19 59128983 1427473 0.024141680231503388 0.3034893555697159
chr20 63025520 1390909 0.022068980946131026 0.16376518177018906
chr21 48129895 914542 0.019001537402065807 0.15681242957009078
chr22 51304566 747606 0.01457191938822755 0.12798676162862002
chrMT 16571 19901 1.200953472934645 1.3256870057743284
chrX 155270560 3912815 0.025199979957565684 0.21064553469321495
chrY 59373566 169518 0.0028551089553893396 0.07403336726435994