BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524412.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 = 1,084,969
number of mapped reads = 999,141 (92.09%)
number of supplementary alignments = 4,037 (0.37%)
number of secondary alignments = 0
number of mapped bases = 58,807,254 bp
number of sequenced bases = 58,790,478 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 42,332
duplication rate = 3.27%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.0304
>>>>>>> ACTG content
number of A's = 15,604,357 bp (26.54%)
number of C's = 10,578,973 bp (17.99%)
number of T's = 18,274,767 bp (31.08%)
number of G's = 14,325,024 bp (24.37%)
number of N's = 7,357 bp (0.01%)
GC percentage = 42.36%
>>>>>>> Mismatches and indels
general error rate = 0.0051
number of mismatches = 290,130
number of insertions = 4,209
mapped reads with insertion percentage = 0.42%
number of deletions = 10,468
mapped reads with deletion percentage = 1.04%
homopolymer indels = 43.35%
>>>>>>> Coverage
mean coverageData = 0.019X
std coverageData = 0.2206X
There is a 1.71% 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 4904230 0.019675898821531923 0.44087024590435764
chr2 243199373 4860597 0.019986058927873963 0.23761572549064713
chr3 198022430 4005020 0.020225082582816502 0.15348351270798832
chr4 191154276 3900792 0.02040651185851579 0.1755320902255322
chr5 180915260 3675750 0.020317523242649627 0.1540445288738947
chr6 171115067 2254472 0.013175181119497795 0.13113811959531305
chr7 159138663 3292009 0.02068641861091921 0.29518063884578777
chr8 146364022 3166043 0.021631292695687195 0.22783734792895333
chr9 141213431 2213279 0.01567328960373465 0.16879131132106223
chr10 135534747 2808564 0.020722095714687836 0.21058201734966894
chr11 135006516 2465083 0.018258992773356214 0.17213131356059505
chr12 133851895 2719962 0.020320683543553868 0.1578229826751643
chr13 115169878 1892117 0.01642892250003078 0.13794627301084894
chr14 107349540 1652987 0.015398174971220185 0.13604984643070314
chr15 102531392 1836333 0.017909958737320177 0.14406738635929495
chr16 90354753 1831493 0.020270023869137243 0.15861062990968616
chr17 81195210 1558317 0.019192228211491785 0.16072486628852758
chr18 78077248 1624705 0.020808942958645264 0.2874445648399842
chr19 59128983 1653543 0.027965016749907572 0.31012558874542023
chr20 63025520 1691360 0.026836113371218516 0.18213576164967932
chr21 48129895 801561 0.01665411902519214 0.15488492184056463
chr22 51304566 420922 0.00820437697494605 0.097543251242512
chrMT 16571 5238 0.3160943817512522 0.5969112472858752
chrX 155270560 3384528 0.021797615723160912 0.17196327307524695
chrY 59373566 188349 0.003172270299547108 0.10107069953071479