BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3082917.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 2,152,816 number of mapped reads = 1,942,916 (90.25%) number of supplementary alignments = 17,117 (0.8%) number of secondary alignments = 0 number of mapped bases = 128,812,994 bp number of sequenced bases = 128,763,014 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 95,226 duplication rate = 3.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.9609 >>>>>>> ACTG content number of A's = 34,417,289 bp (26.73%) number of C's = 24,327,394 bp (18.89%) number of T's = 40,181,887 bp (31.21%) number of G's = 29,830,328 bp (23.17%) number of N's = 6,116 bp (0%) GC percentage = 42.06% >>>>>>> Mismatches and indels general error rate = 0.0076 number of mismatches = 961,499 number of insertions = 10,477 mapped reads with insertion percentage = 0.53% number of deletions = 30,474 mapped reads with deletion percentage = 1.55% homopolymer indels = 46.98% >>>>>>> Coverage mean coverageData = 0.0416X std coverageData = 0.3557X There is a 3.47% of reference with a coverageData >= 1X There is a 0.5% of reference with a coverageData >= 2X There is a 0.09% 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 12688384 0.05090612793297715 0.5171187505058602 chr2 243199373 12318048 0.050649999003081314 0.5535019266102478 chr3 198022430 8457951 0.04271208569655468 0.23837428655453555 chr4 191154276 9266833 0.04847829299931538 0.2616976925830612 chr5 180915260 6892646 0.03809875407967244 0.22697364745519705 chr6 171115067 8814380 0.05151141950579957 0.3571263236239554 chr7 159138663 7468969 0.04693371716966103 0.446248226189808 chr8 146364022 10184100 0.0695806241235978 0.39182881041223666 chr9 141213431 4317024 0.03057091644490955 0.34669302969379145 chr10 135534747 4794123 0.03537191093882368 0.2532722752802049 chr11 135006516 5245969 0.038857154124323896 0.3048568523270577 chr12 133851895 3465871 0.025893327845676 0.19251529585446822 chr13 115169878 2620988 0.022757582499132283 0.176925829509694 chr14 107349540 3027712 0.02820423822961887 0.23103530306697265 chr15 102531392 2853729 0.027832734388312994 0.20204651920059977 chr16 90354753 5055087 0.055947106623156835 0.2947314368579132 chr17 81195210 3559638 0.04384049256107596 0.28392390247645305 chr18 78077248 3401575 0.04356678913683023 0.7218231037683462 chr19 59128983 1899348 0.03212211513937251 0.3723231755287555 chr20 63025520 3069050 0.04869535388204651 0.26665391146470396 chr21 48129895 2911130 0.060484860812598906 0.2932820216138962 chr22 51304566 1955957 0.038124423467494103 0.22652696537720118 chrMT 16571 105784 6.383682336612154 4.315402437419849 chrX 155270560 4219719 0.02717655555567005 0.2246745431772005 chrY 59373566 218979 0.0036881564432225612 0.08386424291174027