BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR5038459.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP093555/SRP093555.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 = 13,086,514
number of mapped reads = 12,339,653 (94.29%)
number of supplementary alignments = 190,152 (1.45%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 6,281,449
number of mapped paired reads (second in pair) = 6,058,204
number of mapped paired reads (both in pair) = 12,077,766
number of mapped paired reads (singletons) = 261,887
number of mapped bases = 1,664,669,953 bp
number of sequenced bases = 1,663,535,235 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 1,896,083
duplication rate = 10.51%
>>>>>>> Insert size
mean insert size = 95,311.8677
std insert size = 3,028,414.721
median insert size = 263
>>>>>>> Mapping quality
mean mapping quality = 53.3579
>>>>>>> ACTG content
number of A's = 476,543,325 bp (28.65%)
number of C's = 328,728,199 bp (19.76%)
number of T's = 487,057,209 bp (29.28%)
number of G's = 371,079,821 bp (22.31%)
number of N's = 126,681 bp (0.01%)
GC percentage = 42.07%
>>>>>>> Mismatches and indels
general error rate = 0.0139
number of mismatches = 22,438,674
number of insertions = 287,628
mapped reads with insertion percentage = 2.22%
number of deletions = 583,947
mapped reads with deletion percentage = 4.56%
homopolymer indels = 47.64%
>>>>>>> Coverage
mean coverageData = 0.5377X
std coverageData = 7.5053X
There is a 25.85% of reference with a coverageData >= 1X
There is a 12.31% of reference with a coverageData >= 2X
There is a 5.75% of reference with a coverageData >= 3X
There is a 3% of reference with a coverageData >= 4X
There is a 1.56% of reference with a coverageData >= 5X
There is a 0.86% of reference with a coverageData >= 6X
There is a 0.49% of reference with a coverageData >= 7X
There is a 0.29% of reference with a coverageData >= 8X
There is a 0.18% of reference with a coverageData >= 9X
There is a 0.12% of reference with a coverageData >= 10X
There is a 0.08% of reference with a coverageData >= 11X
There is a 0.06% of reference with a coverageData >= 12X
There is a 0.05% of reference with a coverageData >= 13X
There is a 0.04% of reference with a coverageData >= 14X
There is a 0.03% of reference with a coverageData >= 15X
There is a 0.03% of reference with a coverageData >= 16X
There is a 0.02% of reference with a coverageData >= 17X
There is a 0.02% of reference with a coverageData >= 18X
There is a 0.02% of reference with a coverageData >= 19X
There is a 0.02% of reference with a coverageData >= 20X
There is a 0.02% of reference with a coverageData >= 21X
There is a 0.02% 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 0.01% of reference with a coverageData >= 28X
There is a 0.01% of reference with a coverageData >= 29X
There is a 0.01% of reference with a coverageData >= 30X
There is a 0.01% of reference with a coverageData >= 31X
There is a 0.01% of reference with a coverageData >= 32X
There is a 0.01% of reference with a coverageData >= 33X
There is a 0.01% of reference with a coverageData >= 34X
There is a 0.01% of reference with a coverageData >= 35X
There is a 0.01% of reference with a coverageData >= 36X
There is a 0.01% of reference with a coverageData >= 37X
There is a 0.01% of reference with a coverageData >= 38X
There is a 0.01% of reference with a coverageData >= 39X
There is a 0.01% of reference with a coverageData >= 40X
There is a 0.01% of reference with a coverageData >= 41X
There is a 0.01% of reference with a coverageData >= 42X
There is a 0.01% of reference with a coverageData >= 43X
There is a 0.01% of reference with a coverageData >= 44X
There is a 0.01% of reference with a coverageData >= 45X
There is a 0.01% of reference with a coverageData >= 46X
There is a 0.01% of reference with a coverageData >= 47X
There is a 0.01% of reference with a coverageData >= 48X
There is a 0.01% of reference with a coverageData >= 49X
There is a 0.01% of reference with a coverageData >= 50X
There is a 0.01% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 143787303 0.5768784142768495 10.510563739713016
chr2 243199373 151371873 0.6224188456275338 8.097398327786342
chr3 198022430 115301939 0.582267064392655 1.3124489523852545
chr4 191154276 72135150 0.3773661333110853 6.551379185856999
chr5 180915260 116285176 0.6427604614447671 1.2947570799812236
chr6 171115067 98690029 0.5767465760335412 6.236385001269946
chr7 159138663 81634044 0.512974298395356 7.8992605328152505
chr8 146364022 106930030 0.7305759198117691 2.923859468895471
chr9 141213431 71386497 0.5055220066142292 12.155824319822733
chr10 135534747 91245263 0.6732241363906483 20.098393413398455
chr11 135006516 76796194 0.5688332406118828 6.215816374666884
chr12 133851895 68652226 0.5128969298492188 1.2730905642021069
chr13 115169878 56804955 0.4932275347204935 1.0998823889575748
chr14 107349540 54196873 0.5048635792943313 1.1743170396819562
chr15 102531392 45092674 0.4397938340679116 1.0555372542126291
chr16 90354753 52867688 0.5851124179377702 8.061148991915566
chr17 81195210 40338171 0.4968048115153591 8.963096590079225
chr18 78077248 67175160 0.8603679269023417 8.17980770419573
chr19 59128983 21818900 0.369005162831906 4.377655880752926
chr20 63025520 44316098 0.7031452973335246 2.331060542485491
chr21 48129895 15988704 0.33219902100347404 2.958996461121642
chr22 51304566 9226779 0.17984323266665972 0.6704372418859992
chrMT 16571 2273854 137.21887635025044 74.33684548099558
chrX 155270560 57043510 0.3673813632152805 1.7074931640667603
chrY 59373566 3310863 0.055763249928427745 6.241750144023905