BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094116.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 = 298,632 number of mapped reads = 285,283 (95.53%) number of supplementary alignments = 23,378 (7.83%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 143,364 number of mapped paired reads (second in pair) = 141,919 number of mapped paired reads (both in pair) = 282,922 number of mapped paired reads (singletons) = 2,361 number of mapped bases = 35,567,203 bp number of sequenced bases = 34,871,884 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 271,812 duplication rate = 52.92% >>>>>>> Insert size mean insert size = 2,000,078.046 std insert size = 12,623,430.8074 median insert size = 147 >>>>>>> Mapping quality mean mapping quality = 40.9409 >>>>>>> ACTG content number of A's = 9,998,396 bp (28.67%) number of C's = 7,514,608 bp (21.55%) number of T's = 9,464,326 bp (27.14%) number of G's = 7,894,212 bp (22.64%) number of N's = 342 bp (0%) GC percentage = 44.19% >>>>>>> Mismatches and indels general error rate = 0.0364 number of mismatches = 1,222,124 number of insertions = 23,837 mapped reads with insertion percentage = 8.25% number of deletions = 95,690 mapped reads with deletion percentage = 32.52% homopolymer indels = 28.27% >>>>>>> Coverage mean coverageData = 0.0115X std coverageData = 2.4844X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% 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% 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 1037910 0.00416412202238806 1.6430847453285984 chr2 243199373 1502301 0.006177240432276937 1.8842167077214504 chr3 198022430 775203 0.003914723195751107 1.158996510323282 chr4 191154276 775998 0.004059537752637037 1.2131612957049134 chr5 180915260 810317 0.0044789864602908565 1.8582439579764416 chr6 171115067 987972 0.005773728855799706 2.193601662144469 chr7 159138663 713999 0.004486646969002121 1.3936401096624802 chr8 146364022 849210 0.0058020406135054145 1.7669570189688957 chr9 141213431 569614 0.004033709796343664 1.3367128809934505 chr10 135534747 580516 0.004283152570462244 1.148763742569086 chr11 135006516 1016087 0.007526207105440748 1.9800688526191135 chr12 133851895 1251328 0.00934860130295503 1.977622535583808 chr13 115169878 882714 0.0076644519845718686 2.3116178265315313 chr14 107349540 106583 9.928594011674387E-4 0.31252902569836283 chr15 102531392 326610 0.0031854634334819135 0.7720252869855648 chr16 90354753 254411 0.0028156902825023492 1.53143840000216 chr17 81195210 324199 0.003992834060038764 1.2742438049710858 chr18 78077248 181728 0.002327541052676447 0.5665002539038636 chr19 59128983 57629 9.746320176012498E-4 0.21442143231128016 chr20 63025520 102868 0.00163216424077104 0.4715989003854707 chr21 48129895 78759 0.0016363842057000124 0.3743439986468895 chr22 51304566 77807 0.001516570669363035 0.5913962860610676 chrMT 16571 190237 11.480115865065477 60.2893515235145 chrX 155270560 21259818 0.136921113699854 8.549041140809726 chrY 59373566 853385 0.014373147134197734 3.7064031083523763