BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013246.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 1,393,560 number of mapped reads = 1,059,885 (76.06%) number of supplementary alignments = 13,732 (0.99%) number of secondary alignments = 0 number of mapped bases = 65,953,830 bp number of sequenced bases = 65,877,058 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 127,385 duplication rate = 9.85% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0654 >>>>>>> ACTG content number of A's = 18,426,700 bp (27.97%) number of C's = 11,121,962 bp (16.88%) number of T's = 22,146,492 bp (33.62%) number of G's = 14,168,124 bp (21.51%) number of N's = 13,780 bp (0.02%) GC percentage = 38.39% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 713,564 number of insertions = 4,665 mapped reads with insertion percentage = 0.44% number of deletions = 43,896 mapped reads with deletion percentage = 4.05% homopolymer indels = 41.92% >>>>>>> Coverage mean coverageData = 0.0213X std coverageData = 0.2994X There is a 1.34% of reference with a coverageData >= 1X There is a 0.46% of reference with a coverageData >= 2X There is a 0.18% of reference with a coverageData >= 3X There is a 0.07% of reference with a coverageData >= 4X There is a 0.03% 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% 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 4017860 0.016119759236226737 0.4300568251904151 chr2 243199373 5913136 0.024313944263334924 0.3047364617097324 chr3 198022430 4419362 0.022317481913538783 0.22238640723944508 chr4 191154276 7696740 0.040264545272322344 0.30544955968231763 chr5 180915260 3741122 0.020678863684578074 0.21212128774998118 chr6 171115067 2453000 0.01433538286841801 0.20778094318244694 chr7 159138663 4766016 0.02994882519529525 0.32101263951602454 chr8 146364022 4813665 0.03288830775639658 0.6783907579247839 chr9 141213431 956249 0.00677165757696235 0.158945902271959 chr10 135534747 3990283 0.02944103330196204 0.3120003698436494 chr11 135006516 3120457 0.02311338069045497 0.2338022626340156 chr12 133851895 1790301 0.013375238355796158 0.16933267910169197 chr13 115169878 1702833 0.014785402481714881 0.1822010657368954 chr14 107349540 2673945 0.02490876998634554 0.24271673239680686 chr15 102531392 1081662 0.010549569052958922 0.14672184136263158 chr16 90354753 2013047 0.0222793702949971 0.22503846951992723 chr17 81195210 1122283 0.013822034575684945 0.1756339464568353 chr18 78077248 2003003 0.025654118854189122 0.3760779804243933 chr19 59128983 475673 0.008044667367270632 0.33421385262610914 chr20 63025520 841293 0.013348449961222057 0.1713683609721707 chr21 48129895 1183601 0.024591805155610665 0.23185630962720405 chr22 51304566 321360 0.006263769973222266 0.10790182409061702 chrMT 16571 39272 2.369923360086899 2.362512784578087 chrX 155270560 4637212 0.029865365333904895 0.2658696442597795 chrY 59373566 180455 0.0030393155095316325 0.07952762365426536