BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR927066.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP026609/SRP026609.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 = 34,561,946
number of mapped reads = 34,136,436 (98.77%)
number of supplementary alignments = 230,130 (0.67%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 17,130,378
number of mapped paired reads (second in pair) = 17,006,058
number of mapped paired reads (both in pair) = 33,892,950
number of mapped paired reads (singletons) = 243,486
number of mapped bases = 3,271,607,474 bp
number of sequenced bases = 3,269,140,102 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 2,278,930
duplication rate = 5.25%
>>>>>>> Insert size
mean insert size = 66,843.8303
std insert size = 2,507,118.1423
median insert size = 194
>>>>>>> Mapping quality
mean mapping quality = 53.8277
>>>>>>> ACTG content
number of A's = 951,644,521 bp (29.11%)
number of C's = 649,076,294 bp (19.85%)
number of T's = 961,225,030 bp (29.4%)
number of G's = 706,614,544 bp (21.61%)
number of N's = 579,713 bp (0.02%)
GC percentage = 41.47%
>>>>>>> Mismatches and indels
general error rate = 0.0103
number of mismatches = 32,833,954
number of insertions = 530,830
mapped reads with insertion percentage = 1.53%
number of deletions = 1,776,032
mapped reads with deletion percentage = 5.06%
homopolymer indels = 53.35%
>>>>>>> Coverage
mean coverageData = 1.0568X
std coverageData = 3.9444X
There is a 35.65% of reference with a coverageData >= 1X
There is a 21.94% of reference with a coverageData >= 2X
There is a 13.97% of reference with a coverageData >= 3X
There is a 9.34% of reference with a coverageData >= 4X
There is a 6.41% of reference with a coverageData >= 5X
There is a 4.49% of reference with a coverageData >= 6X
There is a 3.2% of reference with a coverageData >= 7X
There is a 2.32% of reference with a coverageData >= 8X
There is a 1.69% of reference with a coverageData >= 9X
There is a 1.25% of reference with a coverageData >= 10X
There is a 0.93% of reference with a coverageData >= 11X
There is a 0.7% of reference with a coverageData >= 12X
There is a 0.53% of reference with a coverageData >= 13X
There is a 0.4% of reference with a coverageData >= 14X
There is a 0.31% of reference with a coverageData >= 15X
There is a 0.24% of reference with a coverageData >= 16X
There is a 0.18% of reference with a coverageData >= 17X
There is a 0.14% of reference with a coverageData >= 18X
There is a 0.11% of reference with a coverageData >= 19X
There is a 0.09% of reference with a coverageData >= 20X
There is a 0.07% of reference with a coverageData >= 21X
There is a 0.06% of reference with a coverageData >= 22X
There is a 0.05% of reference with a coverageData >= 23X
There is a 0.04% of reference with a coverageData >= 24X
There is a 0.03% of reference with a coverageData >= 25X
There is a 0.03% of reference with a coverageData >= 26X
There is a 0.02% of reference with a coverageData >= 27X
There is a 0.02% of reference with a coverageData >= 28X
There is a 0.02% of reference with a coverageData >= 29X
There is a 0.02% of reference with a coverageData >= 30X
There is a 0.02% 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 276011405 1.107364964198023 5.9624908527908165
chr2 243199373 274370291 1.1281702235309627 6.194931867055286
chr3 198022430 235968451 1.191624862900632 2.301006206549293
chr4 191154276 205306855 1.0740374701322402 2.944455177759188
chr5 180915260 197313491 1.090640397056611 2.183003228224329
chr6 171115067 180209393 1.0531474297351033 2.1754314068521694
chr7 159138663 162739907 1.022629598188845 3.0794221640378474
chr8 146364022 177585868 1.213316398206111 2.7646369069697254
chr9 141213431 131726176 0.9328161993316344 5.374755108073399
chr10 135534747 154828354 1.1423517395137057 5.8695810314574866
chr11 135006516 157266125 1.1648780344794618 4.230819743996635
chr12 133851895 150956447 1.1277871486242312 2.2541256490776784
chr13 115169878 97117474 0.8432541189285622 1.895486477684565
chr14 107349540 100663679 0.9377187736435573 2.1259897408212836
chr15 102531392 96091015 0.9371862911994797 2.10362568334036
chr16 90354753 103997871 1.1509950229181636 5.481809904853565
chr17 81195210 82294647 1.0135406632977486 3.580175489265794
chr18 78077248 92419890 1.1836980985805237 5.544116675293111
chr19 59128983 43746475 0.7398482568184878 3.277435539321443
chr20 63025520 78242325 1.241438785431679 2.5587785579491653
chr21 48129895 40924292 0.8502884122227983 2.697876583330126
chr22 51304566 39903248 0.777771865373542 2.0104218341076843
chrMT 16571 84110 5.075734717277171 4.4657193953853005
chrX 155270560 186864252 1.2034750953432511 2.739093810226751
chrY 59373566 4975433 0.08379879018888642 3.531688901629249