BamQC report
-----------------------------------
>>>>>>> Input
bam file = SRR1548952.sorted.bam
outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,823,497
number of mapped reads = 9,458,634 (87.39%)
number of secondary alignments = 0
number of mapped bases = 374,184,351 bp
number of sequenced bases = 374,148,609 bp
number of aligned bases = 0 bp
number of duplicated reads (estimated) = 480,803
duplication rate = 3.37%
>>>>>>> Insert size
mean insert size = 0
std insert size = 0
median insert size = 0
>>>>>>> Mapping quality
mean mapping quality = 38.0071
>>>>>>> ACTG content
number of A's = 105,260,416 bp (28.13%)
number of C's = 80,006,131 bp (21.38%)
number of T's = 107,828,981 bp (28.82%)
number of G's = 81,052,573 bp (21.66%)
number of N's = 508 bp (0%)
GC percentage = 43.05%
>>>>>>> Mismatches and indels
general error rate = 0.003
number of mismatches = 1,098,465
number of insertions = 11,807
mapped reads with insertion percentage = 0.12%
number of deletions = 27,476
mapped reads with deletion percentage = 0.29%
homopolymer indels = 39.68%
>>>>>>> Coverage
mean coverageData = 0.1209X
std coverageData = 1.07X
There is a 9.5% of reference with a coverageData >= 1X
There is a 1.76% of reference with a coverageData >= 2X
There is a 0.38% of reference with a coverageData >= 3X
There is a 0.11% of reference with a coverageData >= 4X
There is a 0.04% of reference with a coverageData >= 5X
There is a 0.02% of reference with a coverageData >= 6X
There is a 0.01% of reference with a coverageData >= 7X
There is a 0.01% of reference with a coverageData >= 8X
There is a 0.01% of reference with a coverageData >= 9X
There is a 0.01% of reference with a coverageData >= 10X
There is a 0.01% of reference with a coverageData >= 11X
There is a 0.01% of reference with a coverageData >= 12X
There is a 0.01% 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 30668279 0.12304193617234759 1.9068711661849527
chr2 243199373 32160006 0.1322372077003669 1.0458488831550259
chr3 198022430 25559830 0.12907542847545098 0.4373045888866205
chr4 191154276 25304487 0.13237730031213113 0.5115957066444003
chr5 180915260 23637691 0.13065614807728215 0.465696382034125
chr6 171115067 22506294 0.13152724885412925 0.49489637804199776
chr7 159138663 21762719 0.1367531848624366 1.7384587727800762
chr8 146364022 19618351 0.1340380698201912 2.007276314618047
chr9 141213431 15850594 0.11224565459357758 1.0756914821720849
chr10 135534747 18010062 0.13288151118915653 0.8392386266759846
chr11 135006516 17102836 0.12668155957746513 0.7427136790579489
chr12 133851895 16794494 0.12547072269690318 0.4775626605159234
chr13 115169878 12272306 0.10655829643233623 0.38882725673484325
chr14 107349540 11719873 0.10917487862546965 0.6435472789777428
chr15 102531392 10649388 0.10386465834775753 0.4024953447528401
chr16 90354753 10666925 0.11805604736698246 0.5678503306538082
chr17 81195210 9618265 0.11845852729489831 0.4595078401272696
chr18 78077248 9761905 0.12502880480623496 2.0474206261200423
chr19 59128983 8064719 0.13639197887100477 1.864525743641467
chr20 63025520 7693792 0.12207423278697264 0.4737265439170753
chr21 48129895 4782484 0.09936618394866642 0.6007830065874028
chr22 51304566 4189715 0.08166358916280472 0.49010477206463043
chrMT 16571 7528 0.45428761088648845 0.799044555926837
chrX 155270560 12653219 0.08149142374446257 0.5926375608808295
chrY 59373566 3128589 0.05269329788950187 0.4400981730481693