BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548940.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 = 7,556,545 number of mapped reads = 6,633,595 (87.79%) number of secondary alignments = 0 number of mapped bases = 261,778,931 bp number of sequenced bases = 261,751,128 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 299,130 duplication rate = 2.66% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 34.6174 >>>>>>> ACTG content number of A's = 74,273,236 bp (28.38%) number of C's = 56,666,436 bp (21.65%) number of T's = 74,707,140 bp (28.54%) number of G's = 56,102,102 bp (21.43%) number of N's = 2,214 bp (0%) GC percentage = 43.08% >>>>>>> Mismatches and indels general error rate = 0.0037 number of mismatches = 955,116 number of insertions = 10,218 mapped reads with insertion percentage = 0.15% number of deletions = 21,599 mapped reads with deletion percentage = 0.33% homopolymer indels = 38.02% >>>>>>> Coverage mean coverageData = 0.0846X std coverageData = 0.9232X There is a 6.96% of reference with a coverageData >= 1X There is a 1.02% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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% 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 20605582 0.08267013304652909 1.3740416971413691 chr2 243199373 21845239 0.08982440509828124 0.7903245840728835 chr3 198022430 17375515 0.08774518623976083 0.35117548829493145 chr4 191154276 16993089 0.0888972475823664 0.3981512601958452 chr5 180915260 15984020 0.08835086658803686 0.37130536003697023 chr6 171115067 14973853 0.08750750744818982 0.41550340336592284 chr7 159138663 14987203 0.09417700712993925 1.1963085087188305 chr8 146364022 13498226 0.09222366135852703 2.5866709524401332 chr9 141213431 10988185 0.07781260551625574 0.7798791820294448 chr10 135534747 12204090 0.09004399440093395 0.7121730549548058 chr11 135006516 11811660 0.08748955494859226 0.6859841402260052 chr12 133851895 11868865 0.08867162470878727 0.3918751225229212 chr13 115169878 8119374 0.07049911088731031 0.3015672684864917 chr14 107349540 7955258 0.07410612099502242 0.45495489767735947 chr15 102531392 7362857 0.07181075821149488 0.31579266912915427 chr16 90354753 7343640 0.08127563582626361 0.452887441960312 chr17 81195210 7162027 0.08820750632949899 0.39109413253963243 chr18 78077248 6801426 0.08711149757737363 1.5864476681270383 chr19 59128983 6015098 0.10172841971592848 1.407680714260904 chr20 63025520 5144429 0.08162453875826808 0.383458669574708 chr21 48129895 3231272 0.0671364855460416 0.4225880728161583 chr22 51304566 2948954 0.057479367430961215 0.30321558734714205 chrMT 16571 5295 0.3195341258825659 0.6601252161787564 chrX 155270560 15430077 0.09937541926814716 0.5453957426766392 chrY 59373566 1123697 0.01892588024778569 0.26868241078090327