BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008716.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 = 1,918,921 number of mapped reads = 1,290,506 (67.25%) number of supplementary alignments = 5,128 (0.27%) number of secondary alignments = 0 number of mapped bases = 83,594,487 bp number of sequenced bases = 83,553,181 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,313 duplication rate = 2.43% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.747 >>>>>>> ACTG content number of A's = 25,246,350 bp (30.22%) number of C's = 14,089,965 bp (16.86%) number of T's = 24,970,399 bp (29.89%) number of G's = 19,244,427 bp (23.03%) number of N's = 2,040 bp (0%) GC percentage = 39.9% >>>>>>> Mismatches and indels general error rate = 0.0098 number of mismatches = 811,744 number of insertions = 6,521 mapped reads with insertion percentage = 0.5% number of deletions = 26,742 mapped reads with deletion percentage = 2.05% homopolymer indels = 48.7% >>>>>>> Coverage mean coverageData = 0.027X std coverageData = 0.2224X There is a 2.41% of reference with a coverageData >= 1X There is a 0.21% of reference with a coverageData >= 2X There is a 0.04% 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 7198990 0.02888253586337103 0.2785680062423427 chr2 243199373 7767659 0.03193946967947158 0.30189080747875174 chr3 198022430 6611526 0.033387763194300764 0.20624673242513666 chr4 191154276 4755246 0.024876482491032532 0.17889006659539697 chr5 180915260 4412326 0.024388910034454803 0.17445782047109165 chr6 171115067 4665871 0.02726744688122642 0.19888580754065313 chr7 159138663 4745388 0.02981920238955382 0.272059507237686 chr8 146364022 6359229 0.04344803397108068 0.32933010009390623 chr9 141213431 2831023 0.020047831002703985 0.1865559541474586 chr10 135534747 4444302 0.03279086801261377 0.22961414851620823 chr11 135006516 3456183 0.0256001199231006 0.20567149799802986 chr12 133851895 3854390 0.028795931503248422 0.19118560185073424 chr13 115169878 2524233 0.02191747567884026 0.16726302177670388 chr14 107349540 2910430 0.02711171375303518 0.1854062502229745 chr15 102531392 2154262 0.021010755418204016 0.1657122597756303 chr16 90354753 1890811 0.020926525027410568 0.16944817356849404 chr17 81195210 2157152 0.026567478549535128 0.19266359427050792 chr18 78077248 1525238 0.019534986683956892 0.27877880340031413 chr19 59128983 1368091 0.023137401162472218 0.1979036495334134 chr20 63025520 1768291 0.028056745902294816 0.1892860859008768 chr21 48129895 927233 0.01926521967272108 0.15934080874010972 chr22 51304566 891036 0.01736757699110056 0.14570877569269206 chrMT 16571 21497 1.2972663086114296 1.477977092682739 chrX 155270560 4163466 0.026814265370074017 0.19104972688283411 chrY 59373566 190614 0.003210418589309593 0.07228081668767972