BamQC report
-----------------------------------
>>>>>>> Input
bam file = ERR9714204.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/ERP137498/ERP137498.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 = 113,396
number of mapped reads = 22,418 (19.77%)
number of supplementary alignments = 1,111 (0.98%)
number of secondary alignments = 0
number of mapped bases = 2,468,508 bp
number of sequenced bases = 2,428,793 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 19,549
duplication rate = 52.31%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 31.0853
>>>>>>> ACTG content
number of A's = 437,494 bp (18.01%)
number of C's = 385,652 bp (15.88%)
number of T's = 406,194 bp (16.72%)
number of G's = 1,199,398 bp (49.38%)
number of N's = 55 bp (0%)
GC percentage = 65.26%
>>>>>>> Mismatches and indels
general error rate = 0.0385
number of mismatches = 82,100
number of insertions = 1,951
mapped reads with insertion percentage = 6.4%
number of deletions = 5,155
mapped reads with deletion percentage = 22.23%
homopolymer indels = 37.39%
>>>>>>> Coverage
mean coverageData = 0.0008X
std coverageData = 1.0189X
There is a 0% of reference with a coverageData >= 1X
There is a 0% of reference with a coverageData >= 2X
There is a 0% 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 62779 2.5187098731441074E-4 0.09468493433053708
chr2 243199373 905255 0.0037222752214908054 3.55108967675219
chr3 198022430 19787 9.992302387158869E-5 0.029066635804474432
chr4 191154276 15578 8.149438414864442E-5 0.02594647047384046
chr5 180915260 27259 1.5067275143069745E-4 0.03898894790685179
chr6 171115067 32319 1.8887290620644179E-4 0.04539931697423459
chr7 159138663 73340 4.608559517683016E-4 0.2752032710721426
chr8 146364022 48084 3.285233580148542E-4 0.19136356048916592
chr9 141213431 10260 7.265597845292776E-5 0.022713003613459085
chr10 135534747 25167 1.856867006952837E-4 0.12013319412666158
chr11 135006516 19034 1.4098578767857397E-4 0.04016446285945903
chr12 133851895 26850 2.005948440251817E-4 0.05964813912908417
chr13 115169878 7777 6.752633705142937E-5 0.022790777660624824
chr14 107349540 17851 1.6628855605715684E-4 0.049183764782943964
chr15 102531392 20578 2.0069950869290842E-4 0.062572972666431
chr16 90354753 9276 1.0266200384610647E-4 0.03229706170226736
chr17 81195210 36557 4.502359190893157E-4 0.11278895701827013
chr18 78077248 9432 1.2080343815396773E-4 0.033591761639744894
chr19 59128983 19368 3.275551010238076E-4 0.07714416603508706
chr20 63025520 38136 6.050882245795037E-4 0.2710373728373704
chr21 48129895 3571 7.41950507060113E-5 0.015325794948467314
chr22 51304566 3310 6.451667479264906E-5 0.022081525401743206
chrMT 16571 604 0.03644921851427192 0.29765142584032017
chrX 155270560 1033489 0.006656052506025611 0.8677008380873216
chrY 59373566 2847 4.795063176767924E-5 0.01221911230892316