BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708545.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 20,543,897 number of mapped reads = 19,814,361 (96.45%) number of supplementary alignments = 447 (0%) number of secondary alignments = 0 number of mapped bases = 988,134,981 bp number of sequenced bases = 988,049,313 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 165,498 duplication rate = 0.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.6671 >>>>>>> ACTG content number of A's = 309,917,137 bp (31.37%) number of C's = 182,955,269 bp (18.52%) number of T's = 309,192,732 bp (31.29%) number of G's = 185,566,242 bp (18.78%) number of N's = 417,933 bp (0.04%) GC percentage = 37.3% >>>>>>> Mismatches and indels general error rate = 0.0036 number of mismatches = 3,472,573 number of insertions = 55,306 mapped reads with insertion percentage = 0.28% number of deletions = 51,704 mapped reads with deletion percentage = 0.26% homopolymer indels = 48.36% >>>>>>> Coverage mean coverageData = 0.3192X std coverageData = 0.6245X There is a 25.02% of reference with a coverageData >= 1X There is a 5.55% of reference with a coverageData >= 2X There is a 1.09% of reference with a coverageData >= 3X There is a 0.2% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.01% 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 77163991 0.309583946833978 0.6259739743425594 chr2 243199373 89871948 0.36954021258928166 0.6594250386915015 chr3 198022430 76790159 0.38778515645929607 0.672299856142014 chr4 191154276 83956154 0.43920625662593077 0.7138955959761581 chr5 180915260 70256603 0.38833983932588106 0.6720763762256986 chr6 171115067 66875054 0.39081920237918033 0.6774400440601621 chr7 159138663 56463134 0.3548046272074059 0.6555401226805728 chr8 146364022 55949105 0.3822599586666182 0.6704562044465318 chr9 141213431 40989735 0.2902679632506061 0.6005705834664046 chr10 135534747 42467137 0.31333025618884286 0.6084863809251804 chr11 135006516 44585866 0.3302497340202454 0.6357303402616293 chr12 133851895 46150250 0.34478592925412077 0.6465837214193636 chr13 115169878 42260683 0.3669421530515123 0.6720379062950195 chr14 107349540 32404375 0.30185853614277247 0.617075077960919 chr15 102531392 25650786 0.25017495129686723 0.5594880425932517 chr16 90354753 17809455 0.19710590100334843 0.4918465733556351 chr17 81195210 14904153 0.18355951046865943 0.47645409790803145 chr18 78077248 29744094 0.3809572540261665 0.6708424314477991 chr19 59128983 6441954 0.10894748519520453 0.35621891572990727 chr20 63025520 14598308 0.231625347954289 0.533445970884955 chr21 48129895 13092226 0.272018586369241 0.6022199715828042 chr22 51304566 4799581 0.09355075725618651 0.33749678519189463 chrMT 16571 1982 0.11960654154848832 0.3574208628539195 chrX 155270560 30461612 0.196184080227443 0.4646311128153095 chrY 59373566 4446636 0.07489252035156521 0.30400020184329973