BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1819132.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 744,844
number of mapped reads = 686,266 (92.14%)
number of supplementary alignments = 2,984 (0.4%)
number of secondary alignments = 0
number of mapped bases = 40,571,248 bp
number of sequenced bases = 40,558,657 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 22,716
duplication rate = 2.64%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.2311
>>>>>>> ACTG content
number of A's = 9,897,172 bp (24.4%)
number of C's = 7,436,857 bp (18.34%)
number of T's = 13,097,178 bp (32.29%)
number of G's = 10,127,003 bp (24.97%)
number of N's = 447 bp (0%)
GC percentage = 43.3%
>>>>>>> Mismatches and indels
general error rate = 0.0053
number of mismatches = 207,301
number of insertions = 2,937
mapped reads with insertion percentage = 0.43%
number of deletions = 7,396
mapped reads with deletion percentage = 1.07%
homopolymer indels = 41.82%
>>>>>>> Coverage
mean coverageData = 0.0131X
std coverageData = 0.1559X
There is a 1.2% of reference with a coverageData >= 1X
There is a 0.08% 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 4107744 0.0164803761913195 0.27095056652989535
chr2 243199373 3250650 0.013366193999192588 0.1745541502968101
chr3 198022430 2262787 0.011426922697595418 0.11454348215767726
chr4 191154276 2099349 0.010982485162926724 0.12459320266195933
chr5 180915260 2206609 0.012196920259794557 0.1184938223143436
chr6 171115067 1804481 0.010545424383932247 0.12307984384410012
chr7 159138663 2130541 0.013387953372462354 0.18041573726529603
chr8 146364022 3794668 0.025926234795597514 0.19445571485024085
chr9 141213431 1416831 0.01003325951339572 0.1203053799532762
chr10 135534747 2148669 0.01585327045322186 0.16605607132133718
chr11 135006516 1454162 0.010771050487666833 0.13706709014786722
chr12 133851895 1922037 0.014359430622928424 0.12832995569893793
chr13 115169878 920596 0.007993374795447816 0.09535583447029033
chr14 107349540 997455 0.009291656023863726 0.1028252063002255
chr15 102531392 1105749 0.010784492226536825 0.1111525357377543
chr16 90354753 1321279 0.01462323736306379 0.1332004424875377
chr17 81195210 1515095 0.018659906169341763 0.15146582082588245
chr18 78077248 989072 0.012667864523093847 0.19578602717040508
chr19 59128983 838196 0.014175721574646397 0.1877423897362151
chr20 63025520 1339260 0.021249487509186756 0.15759157662809264
chr21 48129895 514421 0.010688180391833392 0.11914936815355284
chr22 51304566 337990 0.006587912662588355 0.08605540648459807
chrMT 16571 3561 0.2148934886247058 0.500905238536519
chrX 155270560 1942419 0.012509898850110415 0.1223860393043265
chrY 59373566 147627 0.0024864095244001346 0.10090112932211448