BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708519.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,147,914 number of mapped reads = 2,221,114 (70.56%) number of supplementary alignments = 412 (0.01%) number of secondary alignments = 0 number of mapped bases = 107,322,885 bp number of sequenced bases = 107,303,550 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 99,941 duplication rate = 3.42% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.5201 >>>>>>> ACTG content number of A's = 31,470,738 bp (29.33%) number of C's = 19,871,664 bp (18.52%) number of T's = 34,356,866 bp (32.02%) number of G's = 21,602,722 bp (20.13%) number of N's = 1,560 bp (0%) GC percentage = 38.65% >>>>>>> Mismatches and indels general error rate = 0.005 number of mismatches = 524,087 number of insertions = 5,121 mapped reads with insertion percentage = 0.23% number of deletions = 12,743 mapped reads with deletion percentage = 0.57% homopolymer indels = 48.07% >>>>>>> Coverage mean coverageData = 0.0347X std coverageData = 0.3769X There is a 2.97% of reference with a coverageData >= 1X There is a 0.36% of reference with a coverageData >= 2X There is a 0.05% 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 8641994 0.034671905591761795 0.7849605347281012 chr2 243199373 9444329 0.0388336897562643 0.29838651243273784 chr3 198022430 7634748 0.03855496571777248 0.22436795386645508 chr4 191154276 7582545 0.03966714822534234 0.2316408637803774 chr5 180915260 7021049 0.03880849520377662 0.22701935353883704 chr6 171115067 6625538 0.03871978146728599 0.2672069801391809 chr7 159138663 6157087 0.03869007621359745 0.4664826173290351 chr8 146364022 5754453 0.03931603492011172 0.7341219306100925 chr9 141213431 4562366 0.03230830075929534 0.25319322037711517 chr10 135534747 4990709 0.03682235818096152 0.2909650941070622 chr11 135006516 4945504 0.036631594877983516 0.31419978390144854 chr12 133851895 4937771 0.03688981018908996 0.2231314573595375 chr13 115169878 3800571 0.03299969632684685 0.207576939949418 chr14 107349540 3364817 0.03134449388418432 0.20615324485711767 chr15 102531392 2986076 0.029123529308955447 0.1924505045366245 chr16 90354753 2758884 0.030533911149090296 0.20833358884727407 chr17 81195210 2533778 0.031206003408329137 0.25022798670098845 chr18 78077248 2980458 0.03817319483391628 0.42542675779289757 chr19 59128983 1761256 0.02978667838748385 0.533444833149682 chr20 63025520 2025237 0.03213360238836586 0.20579687691057072 chr21 48129895 1463998 0.03041764375343017 0.2293646655019884 chr22 51304566 1022912 0.019938030466917896 0.17840349604581246 chrMT 16571 120737 7.286041880393459 5.369719277113755 chrX 155270560 3469745 0.022346444812203936 0.1954739904145824 chrY 59373566 736323 0.012401528990190685 0.13744351530767177