BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472603.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 9,288,864
number of mapped reads = 8,576,519 (92.33%)
number of supplementary alignments = 279,097 (3%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 4,329,697
number of mapped paired reads (second in pair) = 4,246,822
number of mapped paired reads (both in pair) = 8,382,052
number of mapped paired reads (singletons) = 194,467
number of mapped bases = 698,025,034 bp
number of sequenced bases = 697,732,920 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,310,537
duplication rate = 13.56%
>>>>>>> Insert size
mean insert size = 238,825.8143
std insert size = 4,674,047.4533
median insert size = 126
>>>>>>> Mapping quality
mean mapping quality = 50.4585
>>>>>>> ACTG content
number of A's = 180,959,542 bp (25.94%)
number of C's = 140,813,190 bp (20.18%)
number of T's = 205,948,415 bp (29.52%)
number of G's = 169,569,505 bp (24.3%)
number of N's = 442,268 bp (0.06%)
GC percentage = 44.48%
>>>>>>> Mismatches and indels
general error rate = 0.0117
number of mismatches = 8,021,461
number of insertions = 65,212
mapped reads with insertion percentage = 0.75%
number of deletions = 156,265
mapped reads with deletion percentage = 1.79%
homopolymer indels = 42.8%
>>>>>>> Coverage
mean coverageData = 0.2255X
std coverageData = 1.9015X
There is a 12.39% of reference with a coverageData >= 1X
There is a 5.68% of reference with a coverageData >= 2X
There is a 1.95% of reference with a coverageData >= 3X
There is a 0.93% of reference with a coverageData >= 4X
There is a 0.43% of reference with a coverageData >= 5X
There is a 0.23% of reference with a coverageData >= 6X
There is a 0.13% of reference with a coverageData >= 7X
There is a 0.08% of reference with a coverageData >= 8X
There is a 0.05% of reference with a coverageData >= 9X
There is a 0.03% of reference with a coverageData >= 10X
There is a 0.03% of reference with a coverageData >= 11X
There is a 0.02% of reference with a coverageData >= 12X
There is a 0.02% of reference with a coverageData >= 13X
There is a 0.01% of reference with a coverageData >= 14X
There is a 0.01% of reference with a coverageData >= 15X
There is a 0.01% of reference with a coverageData >= 16X
There is a 0.01% of reference with a coverageData >= 17X
There is a 0.01% of reference with a coverageData >= 18X
There is a 0.01% of reference with a coverageData >= 19X
There is a 0.01% of reference with a coverageData >= 20X
There is a 0.01% of reference with a coverageData >= 21X
There is a 0.01% of reference with a coverageData >= 22X
There is a 0.01% of reference with a coverageData >= 23X
There is a 0.01% of reference with a coverageData >= 24X
There is a 0.01% of reference with a coverageData >= 25X
There is a 0.01% of reference with a coverageData >= 26X
There is a 0.01% 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 42929842 0.1722356471079765 2.1491185342987573
chr2 243199373 65896235 0.2709556122087535 2.9181710111538135
chr3 198022430 34312634 0.1732765020609029 0.6189149371484449
chr4 191154276 32830531 0.17174887053010524 1.1208604884059326
chr5 180915260 30641406 0.16936883046792184 0.6449341202274206
chr6 171115067 43703109 0.25540187527729513 1.1625984240456029
chr7 159138663 56486519 0.35495157452717824 3.614473831818855
chr8 146364022 32585801 0.22263532085774468 1.6899700361548637
chr9 141213431 23169309 0.16407298396425196 2.175810006052619
chr10 135534747 37549525 0.27704722096098355 1.9669892021170776
chr11 135006516 35568578 0.26345823189748857 2.171351842874043
chr12 133851895 34016669 0.25413662615684296 0.7944636488143514
chr13 115169878 36914533 0.3205224633475777 0.9186434933842278
chr14 107349540 16409383 0.15285936949520232 3.0081166656761367
chr15 102531392 19592276 0.19108563355893968 0.6750363871306527
chr16 90354753 24446110 0.2705569899571304 1.1447925977471574
chr17 81195210 20448689 0.2518460017530591 1.4070110059154168
chr18 78077248 14425114 0.18475438581031955 3.5357266146850748
chr19 59128983 11755747 0.1988153085602707 1.5775976281387811
chr20 63025520 23354294 0.3705529760008327 1.1761184180456663
chr21 48129895 10220387 0.2123500788854827 0.9839898864765517
chr22 51304566 6730564 0.13118840143779795 0.5483589496832397
chrMT 16571 39156 2.362923179047734 2.542432893484377
chrX 155270560 42413286 0.27315729395192495 1.1680560826938309
chrY 59373566 1585337 0.026701057504277242 0.8718717794619532