BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3472802.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 = 1,847,316
number of mapped reads = 1,399,385 (75.75%)
number of supplementary alignments = 12,281 (0.66%)
number of secondary alignments = 0
number of mapped bases = 87,648,388 bp
number of sequenced bases = 87,610,111 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 64,849
duplication rate = 3.49%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 42.5853
>>>>>>> ACTG content
number of A's = 23,190,597 bp (26.47%)
number of C's = 17,572,379 bp (20.06%)
number of T's = 25,812,399 bp (29.46%)
number of G's = 21,032,608 bp (24.01%)
number of N's = 2,128 bp (0%)
GC percentage = 44.06%
>>>>>>> Mismatches and indels
general error rate = 0.0092
number of mismatches = 793,472
number of insertions = 6,605
mapped reads with insertion percentage = 0.47%
number of deletions = 21,256
mapped reads with deletion percentage = 1.5%
homopolymer indels = 44.63%
>>>>>>> Coverage
mean coverageData = 0.0283X
std coverageData = 0.2521X
There is a 2.37% of reference with a coverageData >= 1X
There is a 0.3% of reference with a coverageData >= 2X
There is a 0.07% of reference with a coverageData >= 3X
There is a 0.03% of reference with a coverageData >= 4X
There is a 0.01% of reference with a coverageData >= 5X
There is a 0.01% 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 7218102 0.028959213706432452 0.31773164189962155
chr2 243199373 7418216 0.030502611534282204 0.31774947142534177
chr3 198022430 6208373 0.03135186756368963 0.2072807082048176
chr4 191154276 4258075 0.022275593772226158 0.19005545527040024
chr5 180915260 4957045 0.027399816908756067 0.19711476326952862
chr6 171115067 5785400 0.033809997573153505 0.23446394351339028
chr7 159138663 4946864 0.031085242936846842 0.31609066433458644
chr8 146364022 4488294 0.03066528193656772 0.24508235732518077
chr9 141213431 3724833 0.026377328088572537 0.25728772773562814
chr10 135534747 4206838 0.031038815455936182 0.25253337837691026
chr11 135006516 3441252 0.025489525261136285 0.2631227403692853
chr12 133851895 4180842 0.031234836085062525 0.21707411937247417
chr13 115169878 3601076 0.03126751597323043 0.2119345085392676
chr14 107349540 2397029 0.022329196752962334 0.1993551560336629
chr15 102531392 2240215 0.02184906452845193 0.19436413039358577
chr16 90354753 2732597 0.03024298013409433 0.21924296557965817
chr17 81195210 2331455 0.028714193854538956 0.21939444908177538
chr18 78077248 1916427 0.024545268296341592 0.43469746116050195
chr19 59128983 2031374 0.034354962607762086 0.27606560935128677
chr20 63025520 2731257 0.04333573130376393 0.25360049612307095
chr21 48129895 1270728 0.02640205219645711 0.20819934639197274
chr22 51304566 1175584 0.022913827981704396 0.1825849888868426
chrMT 16571 76298 4.604308732122383 3.9001989423132133
chrX 155270560 3910219 0.025183260754646598 0.20710493827155171
chrY 59373566 399995 0.006736920602006624 0.1130900139892055