BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1548944.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 = 5,059,628 number of mapped reads = 4,329,262 (85.56%) number of secondary alignments = 0 number of mapped bases = 170,445,830 bp number of sequenced bases = 170,429,653 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 265,404 duplication rate = 2.72% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 28.8208 >>>>>>> ACTG content number of A's = 47,597,207 bp (27.93%) number of C's = 37,727,915 bp (22.14%) number of T's = 47,900,219 bp (28.11%) number of G's = 37,202,874 bp (21.83%) number of N's = 1,438 bp (0%) GC percentage = 43.97% >>>>>>> Mismatches and indels general error rate = 0.0045 number of mismatches = 763,495 number of insertions = 7,737 mapped reads with insertion percentage = 0.18% number of deletions = 13,181 mapped reads with deletion percentage = 0.3% homopolymer indels = 34.2% >>>>>>> Coverage mean coverageData = 0.0551X std coverageData = 1.0151X There is a 4.61% of reference with a coverageData >= 1X There is a 0.51% of reference with a coverageData >= 2X There is a 0.09% of reference with a coverageData >= 3X There is a 0.03% 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% 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 13302635 0.05337051898458459 1.5104782908223942 chr2 243199373 14286054 0.05874214979986811 0.9842989063855542 chr3 198022430 11018236 0.05564135335577894 0.2894741776473827 chr4 191154276 10762513 0.05630275830188596 0.29603993288742536 chr5 180915260 10336618 0.05713513608525892 0.33167426703844366 chr6 171115067 9505155 0.0555483229305576 0.3547099204174705 chr7 159138663 9974172 0.06267598214017922 1.329167098228313 chr8 146364022 8973957 0.06131258814410006 2.6612712991500818 chr9 141213431 7226592 0.05117496224562379 1.0205270565553333 chr10 135534747 8039719 0.059318508190375714 0.7527622434384263 chr11 135006516 7919162 0.05865762805107866 0.8355341261429586 chr12 133851895 7754138 0.05793073008043704 0.36775211530293017 chr13 115169878 5014090 0.0435364705344222 0.2310091152628963 chr14 107349540 5086082 0.04737870325294361 0.5098658973881883 chr15 102531392 4613921 0.04500008153600411 0.2592233356493119 chr16 90354753 4832289 0.053481292788216686 0.4789522301135866 chr17 81195210 4571538 0.05630305038930252 0.35347668517475656 chr18 78077248 4513384 0.05780664810317085 2.0901781691197514 chr19 59128983 4260247 0.07205006384094244 1.700355214993067 chr20 63025520 3226745 0.05119743557847678 0.3337082054798957 chr21 48129895 1982166 0.04118367596688088 0.3879168560961156 chr22 51304566 1826992 0.03561070958089773 0.2539824413063406 chrMT 16571 4140 0.24983404743226117 0.5877106776835294 chrX 155270560 10529185 0.06781185692896323 0.5833441361757791 chrY 59373566 886100 0.014924149915469117 0.1901612033126448