BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082423.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,568,525 number of mapped reads = 2,347,369 (91.39%) number of supplementary alignments = 21,379 (0.83%) number of secondary alignments = 0 number of mapped bases = 160,643,906 bp number of sequenced bases = 160,584,780 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,415 duplication rate = 2.7% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9389 >>>>>>> ACTG content number of A's = 46,141,285 bp (28.73%) number of C's = 29,843,744 bp (18.58%) number of T's = 50,482,878 bp (31.44%) number of G's = 34,113,360 bp (21.24%) number of N's = 3,513 bp (0%) GC percentage = 39.83% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 1,314,848 number of insertions = 13,310 mapped reads with insertion percentage = 0.56% number of deletions = 36,397 mapped reads with deletion percentage = 1.54% homopolymer indels = 48.23% >>>>>>> Coverage mean coverageData = 0.0519X std coverageData = 0.4313X There is a 4.54% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% 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 12914483 0.051813243024979264 0.7273338888671612 chr2 243199373 14121764 0.058066613518777455 0.49526408669231636 chr3 198022430 11298764 0.057058000954740326 0.26316842566803894 chr4 191154276 11223335 0.058713491713886644 0.27630451216690255 chr5 180915260 10335735 0.05713025534717193 0.2650516958194069 chr6 171115067 7111052 0.04155713535150005 0.2745884267312555 chr7 159138663 8965654 0.05633862840735315 0.5151978351080385 chr8 146364022 8468086 0.0578563357598905 0.8677010809304322 chr9 141213431 6851688 0.048520087299628034 0.38037030798300087 chr10 135534747 7065769 0.05213252805201311 0.3699149866656377 chr11 135006516 7312170 0.0541616080219417 0.3424961272581806 chr12 133851895 7392322 0.0552276230381348 0.26521785254161334 chr13 115169878 5507493 0.0478206028836811 0.24072671697948228 chr14 107349540 4996350 0.04654281704420904 0.25614148125650615 chr15 102531392 4565213 0.04452502702781993 0.23762844055911722 chr16 90354753 4270296 0.04726144290383927 0.27401732667554035 chr17 81195210 4002869 0.04929932443059141 0.2699282242306764 chr18 78077248 4460723 0.057132175047973 0.7129487189748471 chr19 59128983 2778255 0.04698634847144251 0.5349666293652712 chr20 63025520 3162151 0.05017254915151831 0.2523624141819121 chr21 48129895 2183965 0.04537647547329991 0.2521325467373989 chr22 51304566 1579032 0.03077761148978436 0.1913971472826834 chrMT 16571 5767 0.34801762114537443 0.6224709385888733 chrX 155270560 9679113 0.062337077936731856 0.3056152954514422 chrY 59373566 391857 0.006599856239054262 0.14203832696285698