BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525070.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 908,782 number of mapped reads = 814,214 (89.59%) number of supplementary alignments = 11,828 (1.3%) number of secondary alignments = 0 number of mapped bases = 46,576,917 bp number of sequenced bases = 46,561,512 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 40,714 duplication rate = 3.55% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.2463 >>>>>>> ACTG content number of A's = 11,863,998 bp (25.48%) number of C's = 8,591,521 bp (18.45%) number of T's = 14,873,203 bp (31.94%) number of G's = 11,227,904 bp (24.11%) number of N's = 4,886 bp (0.01%) GC percentage = 42.57% >>>>>>> Mismatches and indels general error rate = 0.0056 number of mismatches = 252,098 number of insertions = 4,444 mapped reads with insertion percentage = 0.54% number of deletions = 9,551 mapped reads with deletion percentage = 1.16% homopolymer indels = 42.71% >>>>>>> Coverage mean coverageData = 0.015X std coverageData = 0.2092X There is a 1.37% of reference with a coverageData >= 1X There is a 0.08% 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% 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 3650422 0.014645588385514996 0.3380507853380752 chr2 243199373 3877628 0.015944235185178707 0.3048411239391002 chr3 198022430 2983747 0.015067722378722451 0.13299711213406837 chr4 191154276 3084711 0.016137284838974777 0.17769481703780565 chr5 180915260 2873887 0.01588526584214068 0.13692922257042028 chr6 171115067 2629523 0.015366986941015544 0.15405329101353796 chr7 159138663 2505853 0.015746349458773574 0.28030835857795616 chr8 146364022 2334820 0.01595214430497134 0.20077565276309178 chr9 141213431 2033500 0.014400188322030076 0.17617278998260777 chr10 135534747 2305324 0.017009099518959517 0.21583276947475627 chr11 135006516 2135034 0.01581430336295768 0.22446037493798693 chr12 133851895 2179077 0.01627976204595385 0.14027247095374415 chr13 115169878 1388879 0.01205939455801108 0.12145398093556121 chr14 107349540 1420695 0.013234290524207184 0.1308516512307711 chr15 102531392 1399983 0.013654188953174457 0.13214549837850864 chr16 90354753 1397749 0.01546956804806937 0.1461466140568571 chr17 81195210 1399047 0.017230659296281148 0.15902318946312383 chr18 78077248 1254197 0.01606354004690329 0.29029311558918963 chr19 59128983 1134239 0.0191824540597967 0.2555834014265092 chr20 63025520 1025296 0.016267949871734497 0.14475517827495796 chr21 48129895 654731 0.013603416338223883 0.145015990910904 chr22 51304566 599460 0.01168434014235692 0.12020633192960109 chrMT 16571 119861 7.23317844427011 5.06693233796175 chrX 155270560 1650572 0.010630295917010925 0.14030231060765994 chrY 59373566 538682 0.00907275806880119 0.16544919668981703