BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524915.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 = 2,305,796 number of mapped reads = 2,095,369 (90.87%) number of supplementary alignments = 8,121 (0.35%) number of secondary alignments = 0 number of mapped bases = 121,534,278 bp number of sequenced bases = 121,495,009 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 122,821 duplication rate = 4.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7042 >>>>>>> ACTG content number of A's = 28,904,503 bp (23.79%) number of C's = 23,619,127 bp (19.44%) number of T's = 40,298,513 bp (33.17%) number of G's = 28,671,854 bp (23.6%) number of N's = 1,012 bp (0%) GC percentage = 43.04% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 619,639 number of insertions = 8,727 mapped reads with insertion percentage = 0.41% number of deletions = 23,518 mapped reads with deletion percentage = 1.11% homopolymer indels = 42.32% >>>>>>> Coverage mean coverageData = 0.0393X std coverageData = 0.3532X There is a 3.35% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% 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% 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 11949228 0.04794061475979231 0.6885567232005532 chr2 243199373 10845603 0.04459552204519869 0.4088023448778649 chr3 198022430 7612378 0.03844199871701403 0.22746226995494007 chr4 191154276 5065704 0.02650060519702944 0.23820223038159022 chr5 180915260 7520810 0.041570898994368964 0.2325912697286551 chr6 171115067 7741154 0.045239464506068305 0.26636015829893217 chr7 159138663 7361712 0.04625973262072712 0.44824685217247745 chr8 146364022 10652070 0.07277792625840795 0.43659293938369076 chr9 141213431 4328541 0.03065247384294487 0.27252416436698806 chr10 135534747 5283298 0.03898113300790682 0.4040796913690324 chr11 135006516 7447244 0.05516210787929673 0.3233114163786084 chr12 133851895 4001208 0.029892800546454722 0.20160255068122931 chr13 115169878 3039744 0.026393567943173473 0.18466851585556385 chr14 107349540 2202014 0.020512561115771898 0.17495454960778498 chr15 102531392 3059992 0.02984444022763292 0.1970914155414452 chr16 90354753 3726827 0.04124660713753487 0.25139684580449967 chr17 81195210 2706896 0.03333812425634468 0.21547197490143483 chr18 78077248 3235976 0.04144582554958904 0.4743611976376188 chr19 59128983 2480578 0.04195198148427481 0.48622138417408206 chr20 63025520 2256006 0.03579511918346727 0.2250246689204303 chr21 48129895 1076129 0.022358847863682228 0.20999456377391756 chr22 51304566 2148168 0.04187089312869346 0.2360269294071972 chrMT 16571 38288 2.3105425140305353 2.0693436034171873 chrX 155270560 5413295 0.03486362772182956 0.2395120840179088 chrY 59373566 341415 0.005750286246913315 0.20128015715320605