BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10525061.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 = 794,542
number of mapped reads = 713,104 (89.75%)
number of supplementary alignments = 2,167 (0.27%)
number of secondary alignments = 0
number of mapped bases = 41,906,405 bp
number of sequenced bases = 41,892,676 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 31,650
duplication rate = 3.71%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.4455
>>>>>>> ACTG content
number of A's = 10,978,821 bp (26.21%)
number of C's = 7,756,373 bp (18.51%)
number of T's = 12,914,432 bp (30.83%)
number of G's = 10,238,629 bp (24.44%)
number of N's = 4,421 bp (0.01%)
GC percentage = 42.96%
>>>>>>> Mismatches and indels
general error rate = 0.005
number of mismatches = 203,052
number of insertions = 3,374
mapped reads with insertion percentage = 0.47%
number of deletions = 8,719
mapped reads with deletion percentage = 1.21%
homopolymer indels = 42.48%
>>>>>>> Coverage
mean coverageData = 0.0135X
std coverageData = 0.1589X
There is a 1.23% of reference with a coverageData >= 1X
There is a 0.09% 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 3243497 0.013012994659700367 0.2572531554781768
chr2 243199373 3607286 0.014832628700897185 0.18105864460018803
chr3 198022430 2838384 0.014333648970977681 0.1282794930791077
chr4 191154276 3060969 0.016013081496539475 0.1462078127788752
chr5 180915260 2534341 0.014008442405577064 0.1273063660341661
chr6 171115067 2693604 0.015741477633877794 0.14293666277153325
chr7 159138663 2194163 0.013787743082898717 0.17051100480333176
chr8 146364022 2038704 0.01392899684049404 0.19097081383482845
chr9 141213431 1659952 0.011754915862075471 0.12904615258751112
chr10 135534747 2049069 0.015118403548574891 0.17105921729364917
chr11 135006516 1926606 0.014270466767692901 0.1420304371457247
chr12 133851895 1800165 0.013448931746539711 0.12674566491143707
chr13 115169878 1264371 0.010978313270419544 0.1125341138462284
chr14 107349540 1177998 0.010973479718683472 0.11329173864475374
chr15 102531392 1171529 0.011426051837860544 0.11459854964959261
chr16 90354753 1226648 0.013575910057548385 0.1304047675970206
chr17 81195210 1045871 0.012880944577888277 0.12596454492011921
chr18 78077248 1151547 0.0147488164541865 0.20845507345163186
chr19 59128983 781703 0.013220301793453813 0.1969687626204019
chr20 63025520 914274 0.01450640946714918 0.13157444775590868
chr21 48129895 587895 0.012214757584657104 0.13006507168687245
chr22 51304566 485131 0.009455903008710765 0.10410911879522079
chrMT 16571 13010 0.7851065113752942 1.0434260159821083
chrX 155270560 2292953 0.014767467831635309 0.13701474245132234
chrY 59373566 146735 0.0024713860036636504 0.10367034579323024