BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR9716287.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 = 1,037,369
number of mapped reads = 855,162 (82.44%)
number of supplementary alignments = 2,498 (0.24%)
number of secondary alignments = 0
number of mapped bases = 47,394,858 bp
number of sequenced bases = 47,381,237 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 19,289
duplication rate = 1.55%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 37.8323
>>>>>>> ACTG content
number of A's = 10,336,540 bp (21.82%)
number of C's = 9,777,733 bp (20.64%)
number of T's = 14,345,450 bp (30.28%)
number of G's = 12,920,284 bp (27.27%)
number of N's = 1,230 bp (0%)
GC percentage = 47.91%
>>>>>>> Mismatches and indels
general error rate = 0.0056
number of mismatches = 256,351
number of insertions = 3,507
mapped reads with insertion percentage = 0.41%
number of deletions = 8,114
mapped reads with deletion percentage = 0.94%
homopolymer indels = 36.61%
>>>>>>> Coverage
mean coverageData = 0.0153X
std coverageData = 0.1555X
There is a 1.4% 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 0.01% 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 4723916 0.018952474345088993 0.1767369772896356
chr2 243199373 3909207 0.016074083381785693 0.2100173099635158
chr3 198022430 3199649 0.016158013008930352 0.14706934731695998
chr4 191154276 3045609 0.01593272755248227 0.15328647109309185
chr5 180915260 2832155 0.015654594311170875 0.13597184353820194
chr6 171115067 2049799 0.011979067863147317 0.12277456503797193
chr7 159138663 2803341 0.01761571290818247 0.17400902503318394
chr8 146364022 2846009 0.019444730754939216 0.16279679205062605
chr9 141213431 2101767 0.014883619674958538 0.14189373872954272
chr10 135534747 2431552 0.01794043264787295 0.21180324126144787
chr11 135006516 2009742 0.014886259267663791 0.15304728346718136
chr12 133851895 2329233 0.01740156909993691 0.1424690504092949
chr13 115169878 838354 0.007279281827493123 0.09332930058016235
chr14 107349540 1501013 0.01398248189978271 0.133231245253907
chr15 102531392 965766 0.009419222553810641 0.10727855457387633
chr16 90354753 1345618 0.01489260891455262 0.14125312673349938
chr17 81195210 1817736 0.022387231956170813 0.17040383088667385
chr18 78077248 1188188 0.015218108097252608 0.15909712923184136
chr19 59128983 1344099 0.022731644141418768 0.18966121975356842
chr20 63025520 1238065 0.019643868071219404 0.15711626279121
chr21 48129895 659539 0.01370331267084626 0.13644608763468688
chr22 51304566 542968 0.010583229570638996 0.11424354686643874
chrMT 16571 13226 0.7981413312413252 1.1219841945043978
chrX 155270560 1499363 0.009656453869941604 0.11785037099515863
chrY 59373566 158944 0.002677016233116266 0.08937304914617517