BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525119.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 = 488,740
number of mapped reads = 445,767 (91.21%)
number of supplementary alignments = 11,388 (2.33%)
number of secondary alignments = 0
number of mapped bases = 34,671,020 bp
number of sequenced bases = 34,657,306 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 7,803
duplication rate = 1.06%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.6723
>>>>>>> ACTG content
number of A's = 9,164,897 bp (26.44%)
number of C's = 6,976,321 bp (20.13%)
number of T's = 10,535,502 bp (30.4%)
number of G's = 7,979,335 bp (23.02%)
number of N's = 1,251 bp (0%)
GC percentage = 43.15%
>>>>>>> Mismatches and indels
general error rate = 0.0076
number of mismatches = 258,120
number of insertions = 3,104
mapped reads with insertion percentage = 0.69%
number of deletions = 7,934
mapped reads with deletion percentage = 1.76%
homopolymer indels = 43.11%
>>>>>>> Coverage
mean coverageData = 0.0112X
std coverageData = 0.1446X
There is a 1.06% of reference with a coverageData >= 1X
There is a 0.04% 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 2749158 0.011029693683290763 0.19182770912628544
chr2 243199373 2996185 0.012319871400326348 0.18645603748488676
chr3 198022430 2338009 0.011806788756203022 0.11153296205179489
chr4 191154276 2317197 0.012122130085125587 0.11505813943817911
chr5 180915260 2169137 0.011989795664555882 0.11377584625397202
chr6 171115067 2035598 0.011896076924657955 0.11871789186444454
chr7 159138663 1920536 0.012068318055430691 0.20193962245259164
chr8 146364022 1831487 0.0125132322477446 0.18896590718897815
chr9 141213431 1453017 0.010289509926290227 0.13946953452417002
chr10 135534747 1629007 0.012019109756408075 0.144266861478863
chr11 135006516 1562213 0.01157138963574173 0.14173193214540494
chr12 133851895 1580325 0.011806519437024033 0.11276691278323055
chr13 115169878 1145300 0.009944440507265277 0.10305647568590855
chr14 107349540 1043651 0.009721988561851313 0.11266260861300205
chr15 102531392 983997 0.00959703151206608 0.10102801012975571
chr16 90354753 939433 0.010397161951181472 0.11048466562862302
chr17 81195210 851835 0.010491197695036444 0.11699025975083566
chr18 78077248 964210 0.012349436291606999 0.22195160941071776
chr19 59128983 621363 0.010508602862322188 0.1633997749186153
chr20 63025520 669140 0.010616969126157151 0.10746092228145869
chr21 48129895 441779 0.00917888975240856 0.10195802053651382
chr22 51304566 324875 0.006332282393734702 0.08203155394581585
chrMT 16571 1856 0.1120028966266369 0.34163915878996826
chrX 155270560 2025326 0.013043850682318657 0.13233564332691744
chrY 59373566 76386 0.00128653212441375 0.044569660255377924