BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3081009.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 = 2,709,102
number of mapped reads = 2,209,465 (81.56%)
number of supplementary alignments = 9,280 (0.34%)
number of secondary alignments = 0
number of mapped bases = 138,012,077 bp
number of sequenced bases = 137,964,172 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 70,522
duplication rate = 2.31%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 44.5938
>>>>>>> ACTG content
number of A's = 38,774,942 bp (28.11%)
number of C's = 27,849,370 bp (20.19%)
number of T's = 39,964,983 bp (28.97%)
number of G's = 31,373,109 bp (22.74%)
number of N's = 1,768 bp (0%)
GC percentage = 42.93%
>>>>>>> Mismatches and indels
general error rate = 0.0075
number of mismatches = 1,022,418
number of insertions = 9,491
mapped reads with insertion percentage = 0.43%
number of deletions = 27,432
mapped reads with deletion percentage = 1.23%
homopolymer indels = 45.49%
>>>>>>> Coverage
mean coverageData = 0.0446X
std coverageData = 0.3806X
There is a 3.88% of reference with a coverageData >= 1X
There is a 0.42% of reference with a coverageData >= 2X
There is a 0.06% of reference with a coverageData >= 3X
There is a 0.02% of reference with a coverageData >= 4X
There is a 0.01% 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 11537587 0.0462891003188313 0.6525866071324592
chr2 243199373 11785731 0.04846118990611049 0.402278127150065
chr3 198022430 9643666 0.04869986697971538 0.24559119235954963
chr4 191154276 8493975 0.04443518176909629 0.2601932262465538
chr5 180915260 6740704 0.03725890231702953 0.2170569930641544
chr6 171115067 7870264 0.04599398602345169 0.31172408838425547
chr7 159138663 8493379 0.05337093349841704 0.705587324487603
chr8 146364022 7718360 0.052733997703342694 0.3367593961303431
chr9 141213431 6173926 0.043720529671147215 0.3487434758220331
chr10 135534747 5968406 0.044035984366429665 0.3311637338332668
chr11 135006516 5923763 0.04387760810004163 0.32335823395327656
chr12 133851895 5964724 0.044562118451890426 0.23897974925927998
chr13 115169878 4776299 0.04147177268000579 0.2251931798553821
chr14 107349540 4241030 0.03950673659151217 0.24265540100282976
chr15 102531392 4560016 0.04447434011234335 0.24200267191007152
chr16 90354753 4385083 0.04853184646523244 0.29193851920456326
chr17 81195210 3944279 0.048577730139499606 0.2907542264294759
chr18 78077248 3651733 0.046770769891889635 0.6856174362997213
chr19 59128983 2908077 0.049181921495250476 0.4598145815580556
chr20 63025520 3097161 0.04914137955545626 0.26300558978739724
chr21 48129895 1842283 0.03827731184537178 0.24173440990940068
chr22 51304566 1601737 0.031220164692553874 0.19604690593275212
chrMT 16571 17755 1.071450123710096 1.3257434338250504
chrX 155270560 6298533 0.040564888797979474 0.25945572911596265
chrY 59373566 373606 0.006292463551877615 0.15862096526695002