BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472831.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 3,285,779 number of mapped reads = 2,832,700 (86.21%) number of supplementary alignments = 22,528 (0.69%) number of secondary alignments = 0 number of mapped bases = 184,394,421 bp number of sequenced bases = 184,321,386 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,454 duplication rate = 2.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.505 >>>>>>> ACTG content number of A's = 49,958,028 bp (27.1%) number of C's = 36,618,125 bp (19.87%) number of T's = 54,953,706 bp (29.81%) number of G's = 42,787,835 bp (23.21%) number of N's = 3,692 bp (0%) GC percentage = 43.08% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,551,856 number of insertions = 14,276 mapped reads with insertion percentage = 0.5% number of deletions = 41,259 mapped reads with deletion percentage = 1.44% homopolymer indels = 44.99% >>>>>>> Coverage mean coverageData = 0.0596X std coverageData = 0.4176X There is a 5.05% of reference with a coverageData >= 1X There is a 0.66% of reference with a coverageData >= 2X There is a 0.12% 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% 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 13905632 0.05578975869432237 0.5583800004585907 chr2 243199373 18047466 0.07420852191095081 0.6265842219860077 chr3 198022430 13480978 0.06807803540235316 0.296356044537989 chr4 191154276 10180770 0.05325944160412085 0.2938915248320869 chr5 180915260 9469781 0.05234373816780298 0.2603751367548734 chr6 171115067 11509164 0.06725979308414728 0.32766288441234054 chr7 159138663 11425742 0.07179739847380771 0.5420322144592495 chr8 146364022 10503911 0.07176566246587567 0.42458522300806617 chr9 141213431 10854491 0.07686585421184193 0.5152199413720956 chr10 135534747 7838172 0.05783145778845922 0.3717152887608559 chr11 135006516 6276572 0.04649088196602303 0.4009419400415962 chr12 133851895 7722780 0.05769645622125858 0.28626503742466475 chr13 115169878 7556453 0.06561136584689271 0.30633069057188994 chr14 107349540 3807288 0.03546627214238645 0.2581138362503635 chr15 102531392 3543504 0.03456018621106793 0.23450251114939086 chr16 90354753 6249421 0.06916538192517664 0.33863743800659163 chr17 81195210 4176731 0.051440608380716055 0.288371061984655 chr18 78077248 3191446 0.040875492947702256 0.8207124755094385 chr19 59128983 4327240 0.07318306151147569 0.44511100093354405 chr20 63025520 8125928 0.12893075693782455 0.43435009730303265 chr21 48129895 2307345 0.04793995499055213 0.3019347825754191 chr22 51304566 2169806 0.04229264896227755 0.24699137838458746 chrMT 16571 16146 0.9743527849858186 1.1787752171518031 chrX 155270560 6797483 0.04377831187058255 0.2815819269861901 chrY 59373566 910171 0.015329566022697711 0.20062313718814895