BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094025.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 408,534 number of mapped reads = 379,102 (92.8%) number of supplementary alignments = 20,050 (4.91%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 190,664 number of mapped paired reads (second in pair) = 188,438 number of mapped paired reads (both in pair) = 372,786 number of mapped paired reads (singletons) = 6,316 number of mapped bases = 48,619,727 bp number of sequenced bases = 47,875,066 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 350,146 duplication rate = 43.17% >>>>>>> Insert size mean insert size = 515,346.6709 std insert size = 6,652,520.6184 median insert size = 174 >>>>>>> Mapping quality mean mapping quality = 43.3284 >>>>>>> ACTG content number of A's = 13,423,816 bp (28.04%) number of C's = 10,527,878 bp (21.99%) number of T's = 12,937,408 bp (27.02%) number of G's = 10,985,629 bp (22.95%) number of N's = 335 bp (0%) GC percentage = 44.94% >>>>>>> Mismatches and indels general error rate = 0.0325 number of mismatches = 1,496,731 number of insertions = 27,039 mapped reads with insertion percentage = 7% number of deletions = 112,391 mapped reads with deletion percentage = 28.55% homopolymer indels = 28.09% >>>>>>> Coverage mean coverageData = 0.0157X std coverageData = 6.2926X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.02% 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 0.01% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% 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 778683 0.0031240965293322176 0.8151325885263694 chr2 243199373 1924180 0.007911944740087795 2.1707090939321936 chr3 198022430 752563 0.003800392713088108 1.4185146520735306 chr4 191154276 519623 0.002718343585471245 0.772047930586176 chr5 180915260 1108914 0.006129466359001447 2.72596810290548 chr6 171115067 608575 0.003556524920157966 1.2411473741301733 chr7 159138663 1138870 0.007156463291387587 2.01763440335467 chr8 146364022 904077 0.00617690732767647 1.8510006951830174 chr9 141213431 512367 0.003628316346197976 1.4030118365725806 chr10 135534747 949485 0.007005472921272358 1.6300945423921425 chr11 135006516 1144655 0.008478516696186723 2.307156678564658 chr12 133851895 921508 0.006884534582046822 1.5492427298881157 chr13 115169878 1182966 0.01027148782774607 2.287475783714935 chr14 107349540 575085 0.005357125889873399 0.8753078814644312 chr15 102531392 469185 0.004576013168727876 1.5261008977551984 chr16 90354753 305792 0.0033843488012191233 0.990521804676622 chr17 81195210 2120810 0.02611989056989938 6.379496626408048 chr18 78077248 197782 0.0025331579309762556 0.5597755827308581 chr19 59128983 260965 0.0044134870373129876 0.6489205653089324 chr20 63025520 313718 0.004977634456645498 1.2255695445066737 chr21 48129895 399315 0.008296610661627249 3.095211039149736 chr22 51304566 185876 0.0036229913727366878 0.35595003186040447 chrMT 16571 8770310 529.2565324965301 2256.531780734376 chrX 155270560 21581003 0.1389896642351261 11.06498754207767 chrY 59373566 993420 0.016731688307217392 7.527241688496151