BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR3124845.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 80,086,784
number of mapped reads = 76,014,408 (94.92%)
number of supplementary alignments = 2,529,236 (3.16%)
number of secondary alignments = 0
number of mapped paired reads (first in pair) = 39,067,471
number of mapped paired reads (second in pair) = 36,946,937
number of mapped paired reads (both in pair) = 73,455,830
number of mapped paired reads (singletons) = 2,558,578
number of mapped bases = 9,886,185,145 bp
number of sequenced bases = 9,876,071,951 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 30,588,200
duplication rate = 22.27%
>>>>>>> Insert size
mean insert size = 181,143.9641
std insert size = 4,014,686.7635
median insert size = 255
>>>>>>> Mapping quality
mean mapping quality = 53.0231
>>>>>>> ACTG content
number of A's = 2,864,729,035 bp (29.01%)
number of C's = 1,887,553,511 bp (19.11%)
number of T's = 2,950,807,794 bp (29.88%)
number of G's = 2,172,812,031 bp (22%)
number of N's = 169,580 bp (0%)
GC percentage = 41.11%
>>>>>>> Mismatches and indels
general error rate = 0.0151
number of mismatches = 140,460,526
number of insertions = 2,477,166
mapped reads with insertion percentage = 2.97%
number of deletions = 4,309,068
mapped reads with deletion percentage = 5.36%
homopolymer indels = 42.72%
>>>>>>> Coverage
mean coverageData = 3.1935X
std coverageData = 58.6471X
There is a 45.39% of reference with a coverageData >= 1X
There is a 35.32% of reference with a coverageData >= 2X
There is a 28.1% of reference with a coverageData >= 3X
There is a 23.12% of reference with a coverageData >= 4X
There is a 19.23% of reference with a coverageData >= 5X
There is a 16.23% of reference with a coverageData >= 6X
There is a 13.81% of reference with a coverageData >= 7X
There is a 11.85% of reference with a coverageData >= 8X
There is a 10.24% of reference with a coverageData >= 9X
There is a 8.9% of reference with a coverageData >= 10X
There is a 7.77% of reference with a coverageData >= 11X
There is a 6.82% of reference with a coverageData >= 12X
There is a 6.01% of reference with a coverageData >= 13X
There is a 5.32% of reference with a coverageData >= 14X
There is a 4.72% of reference with a coverageData >= 15X
There is a 4.2% of reference with a coverageData >= 16X
There is a 3.75% of reference with a coverageData >= 17X
There is a 3.36% of reference with a coverageData >= 18X
There is a 3.01% of reference with a coverageData >= 19X
There is a 2.71% of reference with a coverageData >= 20X
There is a 2.44% of reference with a coverageData >= 21X
There is a 2.21% of reference with a coverageData >= 22X
There is a 2% of reference with a coverageData >= 23X
There is a 1.81% of reference with a coverageData >= 24X
There is a 1.65% of reference with a coverageData >= 25X
There is a 1.5% of reference with a coverageData >= 26X
There is a 1.37% of reference with a coverageData >= 27X
There is a 1.25% of reference with a coverageData >= 28X
There is a 1.14% of reference with a coverageData >= 29X
There is a 1.05% of reference with a coverageData >= 30X
There is a 0.96% of reference with a coverageData >= 31X
There is a 0.88% of reference with a coverageData >= 32X
There is a 0.81% of reference with a coverageData >= 33X
There is a 0.75% of reference with a coverageData >= 34X
There is a 0.69% of reference with a coverageData >= 35X
There is a 0.64% of reference with a coverageData >= 36X
There is a 0.59% of reference with a coverageData >= 37X
There is a 0.55% of reference with a coverageData >= 38X
There is a 0.51% of reference with a coverageData >= 39X
There is a 0.47% of reference with a coverageData >= 40X
There is a 0.44% of reference with a coverageData >= 41X
There is a 0.41% of reference with a coverageData >= 42X
There is a 0.38% of reference with a coverageData >= 43X
There is a 0.36% of reference with a coverageData >= 44X
There is a 0.33% of reference with a coverageData >= 45X
There is a 0.31% of reference with a coverageData >= 46X
There is a 0.29% of reference with a coverageData >= 47X
There is a 0.27% of reference with a coverageData >= 48X
There is a 0.26% of reference with a coverageData >= 49X
There is a 0.24% of reference with a coverageData >= 50X
There is a 0.23% of reference with a coverageData >= 51X
>>>>>>> Coverage per contig
chr1 249250621 783837770 3.1447776011759667 22.97975490893996
chr2 243199373 891251398 3.6646944727114903 65.38516442839217
chr3 198022430 648631199 3.275544083566695 8.300016377962816
chr4 191154276 625063798 3.2699441052524505 81.86521912117827
chr5 180915260 560495319 3.0981096840587137 8.458279542363242
chr6 171115067 548905743 3.207816544875034 14.549376733616741
chr7 159138663 604589665 3.7991375169464634 24.87372149861666
chr8 146364022 583384858 3.985848776415833 12.143417858972358
chr9 141213431 399547650 2.829388445352624 53.90200476887887
chr10 135534747 589390866 4.348632945026267 196.78626697231434
chr11 135006516 377876512 2.798950178078812 13.777040564119005
chr12 133851895 433203833 3.236441538612509 19.36778204276683
chr13 115169878 246150285 2.1372800707490547 5.421777818300555
chr14 107349540 319280192 2.974211086512341 8.773019384427819
chr15 102531392 261399446 2.549457691942776 10.1197554315246
chr16 90354753 391768482 4.3358923464712475 91.08915370513343
chr17 81195210 223116904 2.7479072226058654 31.281310205737846
chr18 78077248 207291094 2.6549487758584935 45.82063198841564
chr19 59128983 151069971 2.554922532660506 14.342998698511632
chr20 63025520 210772452 3.344239793658188 26.268496699066137
chr21 48129895 116420077 2.418872449233475 38.95402232561867
chr22 51304566 91273376 1.7790497633290574 8.61284382619478
chrMT 16571 4004037 241.62917144408908 113.24999334145225
chrX 155270560 356869036 2.298368963182718 9.424945390961959
chrY 59373566 260591182 4.389010119419137 136.96451248130745