BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237811.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 = 3,455,026 number of mapped reads = 1,341,361 (38.82%) number of supplementary alignments = 7,125 (0.21%) number of secondary alignments = 0 number of mapped bases = 77,620,508 bp number of sequenced bases = 77,583,464 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 56,557 duplication rate = 2.9% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.1623 >>>>>>> ACTG content number of A's = 20,056,993 bp (25.85%) number of C's = 14,517,038 bp (18.71%) number of T's = 23,529,809 bp (30.33%) number of G's = 19,418,199 bp (25.03%) number of N's = 61,425 bp (0.08%) GC percentage = 43.74% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 695,354 number of insertions = 6,622 mapped reads with insertion percentage = 0.49% number of deletions = 22,770 mapped reads with deletion percentage = 1.68% homopolymer indels = 44.85% >>>>>>> Coverage mean coverageData = 0.0251X std coverageData = 0.2474X There is a 2.2% of reference with a coverageData >= 1X There is a 0.18% of reference with a coverageData >= 2X There is a 0.04% 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 7099897 0.02848497215980858 0.3313900325537069 chr2 243199373 5660612 0.023275602770571287 0.3313960964517255 chr3 198022430 4860211 0.02454373981775701 0.18614119985099817 chr4 191154276 3755152 0.01964461417541086 0.17860132775138357 chr5 180915260 4962528 0.027430123915472913 0.18673000515242108 chr6 171115067 4207027 0.0245859530300742 0.20846650484279988 chr7 159138663 3723346 0.023396866165703554 0.2952712682512085 chr8 146364022 4365278 0.029824802163471567 0.23891187111266188 chr9 141213431 3355654 0.023762994612035168 0.2532593189516957 chr10 135534747 4043128 0.029830933317786027 0.33242112168214577 chr11 135006516 4006690 0.02967775273898632 0.25599206403846997 chr12 133851895 3748838 0.028007358431496245 0.1969997618166584 chr13 115169878 2384064 0.020700412654774195 0.16883097708784614 chr14 107349540 2185201 0.02035594190715675 0.1833873764076836 chr15 102531392 1938364 0.018905078358830825 0.16421592069668078 chr16 90354753 2258970 0.025001119752936517 0.210974020358426 chr17 81195210 2107041 0.0259503116008937 0.20893436592949563 chr18 78077248 1484213 0.01900954552086672 0.37537793203024983 chr19 59128983 1317455 0.02228103601917185 0.26156906621159837 chr20 63025520 2029462 0.03220063872539251 0.21310675446168734 chr21 48129895 1184409 0.02460859305843073 0.19568112980537963 chr22 51304566 812667 0.015840052131032546 0.14404814862256993 chrMT 16571 35326 2.131796511978758 2.398483596707744 chrX 155270560 5808008 0.03740572585041234 0.24524905437240724 chrY 59373566 286967 0.0048332451515544815 0.11155834468397703