BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3080663.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,391,622
number of mapped reads = 1,270,099 (91.27%)
number of supplementary alignments = 12,989 (0.93%)
number of secondary alignments = 0
number of mapped bases = 84,961,567 bp
number of sequenced bases = 84,930,036 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 48,929
duplication rate = 2.95%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 45.3588
>>>>>>> ACTG content
number of A's = 23,293,906 bp (27.43%)
number of C's = 15,822,030 bp (18.63%)
number of T's = 26,738,186 bp (31.48%)
number of G's = 19,072,287 bp (22.46%)
number of N's = 3,627 bp (0%)
GC percentage = 41.09%
>>>>>>> Mismatches and indels
general error rate = 0.0071
number of mismatches = 590,614
number of insertions = 6,552
mapped reads with insertion percentage = 0.51%
number of deletions = 19,292
mapped reads with deletion percentage = 1.5%
homopolymer indels = 47.38%
>>>>>>> Coverage
mean coverageData = 0.0274X
std coverageData = 0.3036X
There is a 2.41% of reference with a coverageData >= 1X
There is a 0.24% of reference with a coverageData >= 2X
There is a 0.03% 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 10184207 0.04085930441874406 0.4209603325532289
chr2 243199373 5691361 0.023402038129432184 0.3373527349399112
chr3 198022430 5212736 0.0263239674414661 0.17727802731139547
chr4 191154276 3646680 0.019077156296519363 0.15909502876986098
chr5 180915260 3913077 0.021629336298109956 0.16124395510957845
chr6 171115067 5104368 0.02983003244243828 0.2612863838586078
chr7 159138663 5504337 0.03458830743098552 0.8022506006237426
chr8 146364022 10157854 0.06940130409917268 0.3770535391612846
chr9 141213431 2699985 0.01911988810752711 0.21155556479861765
chr10 135534747 4067416 0.030010134596702348 0.2298891654457424
chr11 135006516 3559407 0.02636470524133813 0.21312459847529377
chr12 133851895 2684351 0.020054635759919573 0.157966630501612
chr13 115169878 1726314 0.014989283916754692 0.13349530892128306
chr14 107349540 1651899 0.015388039855596959 0.1455461339685322
chr15 102531392 1504880 0.014677260989492857 0.1382153463175712
chr16 90354753 2093023 0.02316450358732097 0.17630699367649227
chr17 81195210 1327233 0.01634619825479853 0.15175903017610531
chr18 78077248 2659800 0.034066262171535557 0.3513981541492979
chr19 59128983 1389909 0.02350639110434218 0.26721852755805114
chr20 63025520 2138391 0.033928970359943085 0.20695178867359965
chr21 48129895 1208569 0.025110567974436677 0.1802986835326848
chr22 51304566 822122 0.016024343720206113 0.1370752182028634
chrMT 16571 106050 6.399734475891618 3.854407517126854
chrX 155270560 5710778 0.03677952858545754 0.2265021909914246
chrY 59373566 196820 0.0033149432190075967 0.07890701597523166