BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238631.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 = 4,100,073 number of mapped reads = 3,793,120 (92.51%) number of supplementary alignments = 20,649 (0.5%) number of secondary alignments = 0 number of mapped bases = 235,385,743 bp number of sequenced bases = 235,260,444 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 478,279 duplication rate = 10.61% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.3862 >>>>>>> ACTG content number of A's = 58,371,606 bp (24.81%) number of C's = 41,504,600 bp (17.64%) number of T's = 78,338,441 bp (33.3%) number of G's = 57,033,749 bp (24.24%) number of N's = 12,048 bp (0.01%) GC percentage = 41.88% >>>>>>> Mismatches and indels general error rate = 0.0059 number of mismatches = 1,350,640 number of insertions = 14,876 mapped reads with insertion percentage = 0.39% number of deletions = 72,208 mapped reads with deletion percentage = 1.88% homopolymer indels = 42.09% >>>>>>> Coverage mean coverageData = 0.076X std coverageData = 0.787X There is a 5.57% of reference with a coverageData >= 1X There is a 1.34% of reference with a coverageData >= 2X There is a 0.37% of reference with a coverageData >= 3X There is a 0.11% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% 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 18577707 0.07453424559371509 1.1517915992919034 chr2 243199373 21887015 0.08999618185693267 1.556797994504281 chr3 198022430 21433368 0.10823707193169986 0.4348098698562935 chr4 191154276 9755807 0.051036300124408414 0.31813245633185006 chr5 180915260 5943318 0.032851391308837075 0.25633209821462444 chr6 171115067 14634537 0.08552453770771688 0.6840366366434292 chr7 159138663 23365024 0.14682179402248716 1.5160253965333526 chr8 146364022 12880547 0.08800350539697523 0.746547201350728 chr9 141213431 8304965 0.05881143841055742 0.49032510205195884 chr10 135534747 15351874 0.11326891693685015 0.6228557413752088 chr11 135006516 5622646 0.041647219457170495 0.3408436817697543 chr12 133851895 9262593 0.0692003127785378 0.35989251019683594 chr13 115169878 10046138 0.08722886725641925 0.4705303537394406 chr14 107349540 6519664 0.060733040868176984 0.3481461992396499 chr15 102531392 2786533 0.027177364372464582 0.37988225524077884 chr16 90354753 6698258 0.07413287931847924 0.44535019495545347 chr17 81195210 4054810 0.04993902965458184 0.3039288591593501 chr18 78077248 5509427 0.0705637959985475 1.1996610125579816 chr19 59128983 7059032 0.11938361936649579 0.7554843781428003 chr20 63025520 4955882 0.07863294106895112 0.37709981673801696 chr21 48129895 3771167 0.078353941973071 0.40028897210282083 chr22 51304566 2305573 0.044938943641000685 0.2725409774011356 chrMT 16571 12744 0.76905437209583 1.2015117239106832 chrX 155270560 14044387 0.0904510616822661 0.43334281054685975 chrY 59373566 602727 0.010151436752173518 0.2705841724262724