BamQC report ----------------------------------- >>>>>>> Input bam file = SRR054612.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP002535/SRP002535.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 = 17,877,465 number of mapped reads = 15,020,338 (84.02%) number of supplementary alignments = 481 (0%) number of secondary alignments = 0 number of mapped bases = 712,328,040 bp number of sequenced bases = 712,173,757 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,228,170 duplication rate = 19.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0026 >>>>>>> ACTG content number of A's = 212,589,202 bp (29.85%) number of C's = 129,907,334 bp (18.24%) number of T's = 223,702,594 bp (31.41%) number of G's = 145,970,334 bp (20.5%) number of N's = 4,293 bp (0%) GC percentage = 38.74% >>>>>>> Mismatches and indels general error rate = 0.0042 number of mismatches = 2,918,741 number of insertions = 29,180 mapped reads with insertion percentage = 0.19% number of deletions = 103,334 mapped reads with deletion percentage = 0.69% homopolymer indels = 49.98% >>>>>>> Coverage mean coverageData = 0.2301X std coverageData = 1.5668X There is a 8.08% of reference with a coverageData >= 1X There is a 3.95% of reference with a coverageData >= 2X There is a 2.45% of reference with a coverageData >= 3X There is a 1.68% of reference with a coverageData >= 4X There is a 1.22% of reference with a coverageData >= 5X There is a 0.92% of reference with a coverageData >= 6X There is a 0.71% of reference with a coverageData >= 7X There is a 0.56% of reference with a coverageData >= 8X There is a 0.45% of reference with a coverageData >= 9X There is a 0.37% of reference with a coverageData >= 10X There is a 0.31% of reference with a coverageData >= 11X There is a 0.26% of reference with a coverageData >= 12X There is a 0.22% of reference with a coverageData >= 13X There is a 0.19% of reference with a coverageData >= 14X There is a 0.16% of reference with a coverageData >= 15X There is a 0.14% of reference with a coverageData >= 16X There is a 0.12% of reference with a coverageData >= 17X There is a 0.1% of reference with a coverageData >= 18X There is a 0.09% of reference with a coverageData >= 19X There is a 0.08% 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 0.06% of reference with a coverageData >= 23X There is a 0.05% of reference with a coverageData >= 24X There is a 0.05% of reference with a coverageData >= 25X There is a 0.04% of reference with a coverageData >= 26X There is a 0.04% of reference with a coverageData >= 27X There is a 0.03% of reference with a coverageData >= 28X There is a 0.03% of reference with a coverageData >= 29X There is a 0.03% of reference with a coverageData >= 30X There is a 0.03% of reference with a coverageData >= 31X There is a 0.02% of reference with a coverageData >= 32X There is a 0.02% of reference with a coverageData >= 33X There is a 0.02% of reference with a coverageData >= 34X There is a 0.02% of reference with a coverageData >= 35X There is a 0.02% of reference with a coverageData >= 36X There is a 0.02% 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 62717306 0.25162346937542834 1.7476131081080946 chr2 243199373 58584196 0.24088958485925044 1.7085942935313756 chr3 198022430 52962646 0.2674578127336383 1.5568761615105078 chr4 191154276 46765504 0.24464796173327558 1.5379037357752212 chr5 180915260 35236242 0.19476655534751464 1.2345268712462678 chr6 171115067 35695517 0.2086053415740415 1.3893568632283861 chr7 159138663 50741755 0.3188524651611532 1.9831233781512994 chr8 146364022 36887061 0.25202273411152915 1.6159866473901647 chr9 141213431 34456586 0.2440036033116425 1.664371362165359 chr10 135534747 29985133 0.22123576177849064 1.593309074145405 chr11 135006516 31662938 0.23452896155027064 1.5987562722119832 chr12 133851895 24802259 0.1852962858687955 1.207713708588946 chr13 115169878 23317729 0.2024637813717229 1.2771665857028245 chr14 107349540 14612650 0.1361221482644453 1.3116686215411262 chr15 102531392 18090933 0.17644286932142694 1.160508432890609 chr16 90354753 18371185 0.20332284013880267 1.432349539033279 chr17 81195210 12312781 0.15164417950270712 1.0403250990855162 chr18 78077248 27777851 0.3557739509466317 2.3796041258966936 chr19 59128983 12002583 0.2029898434072509 1.4748795550840847 chr20 63025520 12577381 0.19956013056298463 1.3296569320674088 chr21 48129895 8933217 0.18560640948832322 1.478259488071059 chr22 51304566 5977194 0.11650413337479552 0.8623521276789075 chrMT 16571 89500 5.40100175004526 11.748115706050328 chrX 155270560 55744376 0.35901445837510987 2.0496226438891476 chrY 59373566 2023517 0.03408110942839445 0.7221877624388101