BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548984.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 = 5,013,827 number of mapped reads = 2,173,506 (43.35%) number of secondary alignments = 0 number of mapped bases = 85,777,973 bp number of sequenced bases = 85,766,351 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 44,897 duplication rate = 1.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.093 >>>>>>> ACTG content number of A's = 26,008,638 bp (30.32%) number of C's = 16,803,684 bp (19.59%) number of T's = 26,128,296 bp (30.46%) number of G's = 16,821,269 bp (19.61%) number of N's = 4,464 bp (0.01%) GC percentage = 39.21% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 265,578 number of insertions = 3,896 mapped reads with insertion percentage = 0.18% number of deletions = 9,348 mapped reads with deletion percentage = 0.43% homopolymer indels = 45.12% >>>>>>> Coverage mean coverageData = 0.0277X std coverageData = 0.2387X There is a 2.45% of reference with a coverageData >= 1X There is a 0.25% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% 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 6843780 0.0274574240679625 0.3498848040271996 chr2 243199373 7328974 0.030135661575081445 0.2299483184479859 chr3 198022430 6084100 0.030724297242489148 0.19397745811697986 chr4 191154276 6068513 0.03174667670002841 0.1991739712329262 chr5 180915260 5425306 0.02998810603373093 0.19205890130567946 chr6 171115067 5315816 0.03106573893928347 0.21112902364158845 chr7 159138663 4816269 0.030264606408060623 0.31873241147593717 chr8 146364022 4381273 0.02993408448423206 0.4156512540982928 chr9 141213431 3691843 0.026143710083780913 0.20746313321307297 chr10 135534747 4026322 0.029706935594899512 0.20733720616342205 chr11 135006516 3931486 0.02912071295877304 0.2132212065882499 chr12 133851895 4056419 0.03030527883075544 0.1967338022142653 chr13 115169878 2923146 0.025381167808478534 0.17659388578604907 chr14 107349540 2691552 0.02507278559367837 0.18943357346313436 chr15 102531392 2482317 0.024210312096416286 0.17210619405527047 chr16 90354753 2299421 0.025448810645301637 0.18094045857432292 chr17 81195210 2172761 0.026759718953864396 0.18745579852524225 chr18 78077248 2393184 0.030651490175473396 0.29272050919391956 chr19 59128983 1557141 0.026334648779601028 0.3047273417600263 chr20 63025520 1654315 0.0262483355948511 0.1821189877334802 chr21 48129895 1134370 0.0235689273787113 0.18005999114733234 chr22 51304566 898032 0.01750393912307922 0.16591988538962618 chrMT 16571 4636 0.2797658560135176 0.5720653764863184 chrX 155270560 2923898 0.018830987664371145 0.16464527117565453 chrY 59373566 673099 0.011336678009200256 0.14484297315850495