BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081779.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 = 2,951,393 number of mapped reads = 2,666,308 (90.34%) number of supplementary alignments = 18,347 (0.62%) number of secondary alignments = 0 number of mapped bases = 178,409,218 bp number of sequenced bases = 178,347,363 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 119,683 duplication rate = 3.09% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9244 >>>>>>> ACTG content number of A's = 48,772,211 bp (27.35%) number of C's = 34,287,618 bp (19.23%) number of T's = 54,497,241 bp (30.56%) number of G's = 40,788,210 bp (22.87%) number of N's = 2,083 bp (0%) GC percentage = 42.1% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 1,506,346 number of insertions = 12,965 mapped reads with insertion percentage = 0.48% number of deletions = 34,522 mapped reads with deletion percentage = 1.28% homopolymer indels = 46.22% >>>>>>> Coverage mean coverageData = 0.0576X std coverageData = 0.5503X There is a 4.86% of reference with a coverageData >= 1X There is a 0.62% of reference with a coverageData >= 2X There is a 0.1% of reference with a coverageData >= 3X There is a 0.03% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 14182143 0.05689912804670605 1.0306755617167678 chr2 243199373 15265925 0.06277123502287976 0.7256730603362312 chr3 198022430 12021985 0.06071021853433472 0.2878852497833049 chr4 191154276 11762067 0.06153180167416187 0.340941012133703 chr5 180915260 10917187 0.06034420203138199 0.2836592225227819 chr6 171115067 10379392 0.060657382087808784 0.34843030306973805 chr7 159138663 9947165 0.06250627479508232 0.7967219973884025 chr8 146364022 8981461 0.06136385757423365 0.5872071006576316 chr9 141213431 7500817 0.05311688092898189 0.5229498464932791 chr10 135534747 8537037 0.06298781079364098 0.6397978655470408 chr11 135006516 8011991 0.05934521708567014 0.43654459569553095 chr12 133851895 8076246 0.060337180881899356 0.2888282066775375 chr13 115169878 5649276 0.04905167998875539 0.2516199461032662 chr14 107349540 5389859 0.05020849646863881 0.29743064182834167 chr15 102531392 4991912 0.048686669542143735 0.261734788357656 chr16 90354753 5064559 0.05605193785433733 0.33976945649803847 chr17 81195210 4667412 0.05748383432963595 0.32121182936335335 chr18 78077248 4761115 0.06097954425852715 0.9572800512041058 chr19 59128983 3619752 0.06121789715206162 0.7843026750995298 chr20 63025520 3508365 0.05566578427278347 0.28829880581996503 chr21 48129895 2326156 0.04833079315880494 0.29790490405188313 chr22 51304566 1904777 0.03712685143852498 0.2176746848982713 chrMT 16571 53977 3.2573169995775753 2.4612304047798506 chrX 155270560 10351888 0.06666999848522476 0.37338653207807165 chrY 59373566 536754 0.009040285705594979 0.2422959635970295