BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR10524474.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 = 1,767,783
number of mapped reads = 1,632,598 (92.35%)
number of supplementary alignments = 4,058 (0.23%)
number of secondary alignments = 0
number of mapped bases = 95,653,290 bp
number of sequenced bases = 95,622,970 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 67,261
duplication rate = 3.12%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.5307
>>>>>>> ACTG content
number of A's = 23,951,333 bp (25.05%)
number of C's = 17,054,335 bp (17.83%)
number of T's = 31,244,155 bp (32.67%)
number of G's = 23,371,245 bp (24.44%)
number of N's = 1,902 bp (0%)
GC percentage = 42.28%
>>>>>>> Mismatches and indels
general error rate = 0.0047
number of mismatches = 442,385
number of insertions = 6,301
mapped reads with insertion percentage = 0.38%
number of deletions = 17,797
mapped reads with deletion percentage = 1.08%
homopolymer indels = 43.28%
>>>>>>> Coverage
mean coverageData = 0.0309X
std coverageData = 0.2801X
There is a 2.73% of reference with a coverageData >= 1X
There is a 0.26% of reference with a coverageData >= 2X
There is a 0.04% of reference with a coverageData >= 3X
There is a 0.01% of reference with a coverageData >= 4X
There is a 0.01% 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 9257587 0.03714168078241217 0.5133477703778996
chr2 243199373 7501533 0.030845198766199122 0.3146649939792158
chr3 198022430 5201260 0.02626601441058975 0.17958907637936372
chr4 191154276 5439751 0.028457385907495997 0.20579848808540832
chr5 180915260 5600719 0.03095769256833282 0.1947533549612319
chr6 171115067 4142575 0.024209294205518442 0.22388529882852776
chr7 159138663 4874937 0.030633266034162925 0.3595320080065114
chr8 146364022 8143102 0.05563595403247391 0.30075897718404937
chr9 141213431 4523703 0.03203450952197316 0.25150575151898397
chr10 135534747 5036739 0.03716197588799867 0.2771981618794868
chr11 135006516 3278276 0.024282353897644465 0.25679117267356305
chr12 133851895 4433375 0.03312149596387858 0.20203812176177796
chr13 115169878 2160275 0.018757291728658424 0.15334059922937165
chr14 107349540 2299958 0.021424945090589117 0.16630321545214388
chr15 102531392 2529363 0.02466915693488293 0.18431430900530074
chr16 90354753 2973057 0.03290426791383072 0.21382622663581455
chr17 81195210 3277755 0.04036882224948984 0.2350398612482452
chr18 78077248 2327372 0.029808581368031824 0.41615268198219246
chr19 59128983 1934666 0.03271941951039476 0.37042382683943254
chr20 63025520 2702650 0.04288183580238608 0.23354451168139428
chr21 48129895 1292362 0.026851544139042897 0.19290056661299254
chr22 51304566 777488 0.015154362674074662 0.13537656399067682
chrMT 16571 9928 0.5991189427312775 0.9131676548801635
chrX 155270560 5650611 0.0363920307880644 0.23863547930272117
chrY 59373566 284248 0.004787450361327463 0.1287959215449687