BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR6013291.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,505,137
number of mapped reads = 2,241,431 (89.47%)
number of supplementary alignments = 14,564 (0.58%)
number of secondary alignments = 0
number of mapped bases = 149,995,946 bp
number of sequenced bases = 149,924,676 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 103,790
duplication rate = 3.51%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 46.3308
>>>>>>> ACTG content
number of A's = 42,119,944 bp (28.09%)
number of C's = 27,186,116 bp (18.13%)
number of T's = 48,050,460 bp (32.05%)
number of G's = 32,565,888 bp (21.72%)
number of N's = 2,268 bp (0%)
GC percentage = 39.85%
>>>>>>> Mismatches and indels
general error rate = 0.0075
number of mismatches = 1,102,881
number of insertions = 10,589
mapped reads with insertion percentage = 0.47%
number of deletions = 41,358
mapped reads with deletion percentage = 1.82%
homopolymer indels = 47.08%
>>>>>>> Coverage
mean coverageData = 0.0485X
std coverageData = 0.4367X
There is a 3.96% of reference with a coverageData >= 1X
There is a 0.64% of reference with a coverageData >= 2X
There is a 0.12% 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 10697262 0.04291769447587455 0.7082076421398696
chr2 243199373 12667729 0.05208783576921475 0.5171009087188004
chr3 198022430 10453050 0.05278720193464952 0.26980373339172165
chr4 191154276 9485736 0.04962345702379161 0.27886690513976575
chr5 180915260 7292714 0.040310109827109114 0.24098693796010992
chr6 171115067 9431048 0.05511524008578391 0.42213124709296407
chr7 159138663 9734143 0.061167681168717625 0.6412594671484546
chr8 146364022 10574132 0.07224543200924063 0.6658427002253091
chr9 141213431 4336277 0.0307072561674392 0.37265239790560817
chr10 135534747 7788210 0.05746282907068842 0.4163247646388936
chr11 135006516 7949974 0.0588858540724064 0.4528643320562293
chr12 133851895 7514535 0.05614066950639735 0.2847276497991339
chr13 115169878 2124091 0.0184431123561666 0.15888728000926153
chr14 107349540 6841320 0.06372938347011081 0.3095458294816957
chr15 102531392 2669961 0.026040424770591236 0.2019161241113381
chr16 90354753 4469624 0.04946750283297216 0.2761860073302653
chr17 81195210 3184165 0.03921616804735156 0.28300700440435733
chr18 78077248 3945996 0.05053963992173495 0.7413591263900271
chr19 59128983 2351420 0.03976763814794514 0.5003294020313938
chr20 63025520 3091150 0.049046005491109 0.2745941241032533
chr21 48129895 3939148 0.08184410125972641 0.3545935831055806
chr22 51304566 780632 0.015215643769406411 0.13906716398507624
chrMT 16571 33818 2.0407941584696156 2.036488210105162
chrX 155270560 8332753 0.05366602013929749 0.32368900267572726
chrY 59373566 307058 0.005171628060878135 0.11609423114892069