BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234108.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 5,178,341 number of mapped reads = 4,885,807 (94.35%) number of supplementary alignments = 43,498 (0.84%) number of secondary alignments = 0 number of mapped bases = 318,073,130 bp number of sequenced bases = 317,951,222 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 768,290 duplication rate = 13.26% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9494 >>>>>>> ACTG content number of A's = 83,274,781 bp (26.19%) number of C's = 57,282,339 bp (18.02%) number of T's = 103,386,040 bp (32.52%) number of G's = 73,976,700 bp (23.27%) number of N's = 31,362 bp (0.01%) GC percentage = 41.28% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 1,722,903 number of insertions = 22,449 mapped reads with insertion percentage = 0.45% number of deletions = 69,565 mapped reads with deletion percentage = 1.41% homopolymer indels = 45.03% >>>>>>> Coverage mean coverageData = 0.1027X std coverageData = 1.0295X There is a 7.01% of reference with a coverageData >= 1X There is a 2.03% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.22% of reference with a coverageData >= 4X There is a 0.08% of reference with a coverageData >= 5X There is a 0.04% of reference with a coverageData >= 6X There is a 0.02% 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 22853957 0.09169067225714153 1.7184037153662592 chr2 243199373 32438301 0.1333815157492203 1.9027229066214322 chr3 198022430 44284283 0.22363266120913677 0.6539069863322768 chr4 191154276 7049146 0.036876737196294786 0.4268698606963858 chr5 180915260 10940303 0.060471974558696705 0.36113718490315894 chr6 171115067 24867800 0.1453279388892154 0.8216148272791185 chr7 159138663 12694293 0.07976875487511165 0.8244092017444251 chr8 146364022 19957937 0.1363582165021401 1.6301478601325807 chr9 141213431 12876752 0.09118645378710472 0.780688221571855 chr10 135534747 15535024 0.11462023092867839 0.7752842356969633 chr11 135006516 7700593 0.05703867656284086 0.5500959248388319 chr12 133851895 2819240 0.021062383913204964 0.282976465650435 chr13 115169878 23554905 0.20452313928820867 0.6773852134333446 chr14 107349540 16656903 0.15516510829948596 0.6374153431698146 chr15 102531392 5836817 0.05692712140297481 0.36430607095099904 chr16 90354753 8898943 0.0984889306265936 0.61913202543921 chr17 81195210 6838167 0.08421884739259865 0.433457518551014 chr18 78077248 5911031 0.07570747114447476 2.112030020805465 chr19 59128983 8446970 0.14285667656418174 1.0128213534349204 chr20 63025520 7612129 0.12077851955842649 0.5874844969304224 chr21 48129895 6349585 0.13192600981157346 0.5597609510556311 chr22 51304566 2505817 0.04884198806008806 0.2897594677581421 chrMT 16571 570517 34.42864039587231 20.920706969393198 chrX 155270560 10007757 0.06445366719872718 0.4792980396840137 chrY 59373566 865960 0.014584941723055678 0.3721986053125416