BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1819079.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 1,919,652 number of mapped reads = 1,766,167 (92%) number of supplementary alignments = 8,654 (0.45%) number of secondary alignments = 0 number of mapped bases = 103,102,966 bp number of sequenced bases = 103,072,871 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 83,562 duplication rate = 3.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.1081 >>>>>>> ACTG content number of A's = 25,519,928 bp (24.76%) number of C's = 18,625,939 bp (18.07%) number of T's = 32,025,873 bp (31.07%) number of G's = 26,899,637 bp (26.1%) number of N's = 1,494 bp (0%) GC percentage = 44.17% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 510,220 number of insertions = 5,488 mapped reads with insertion percentage = 0.31% number of deletions = 18,064 mapped reads with deletion percentage = 1.02% homopolymer indels = 44.74% >>>>>>> Coverage mean coverageData = 0.0333X std coverageData = 0.2918X There is a 2.9% of reference with a coverageData >= 1X There is a 0.31% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 10039208 0.04027756464446281 0.5268814970800927 chr2 243199373 8149950 0.03351139396235203 0.33868344692809355 chr3 198022430 5451881 0.02753163366392383 0.18603160167275548 chr4 191154276 6023389 0.0315106160638541 0.2229597224353463 chr5 180915260 5686746 0.031433202483859016 0.199435714471177 chr6 171115067 4230247 0.024721651191592614 0.23443380295151373 chr7 159138663 5164267 0.03245136601405279 0.34391767795661127 chr8 146364022 9319834 0.06367571670037873 0.33315823280492984 chr9 141213431 4318889 0.030584123403955818 0.2553290962955828 chr10 135534747 5332853 0.03934675880569578 0.3055665319710538 chr11 135006516 3921711 0.029048309046061156 0.27200715484322696 chr12 133851895 4922845 0.03677829888026613 0.21624992804246754 chr13 115169878 2394899 0.02079449107343849 0.16008620235364 chr14 107349540 2379727 0.02216802233153491 0.1709015306155725 chr15 102531392 2729104 0.026617252987260722 0.18460892270238616 chr16 90354753 3182049 0.03521728403153291 0.22003014687893874 chr17 81195210 3556517 0.043802054333008066 0.25164736835020557 chr18 78077248 2362794 0.030262260268189782 0.4314803123271366 chr19 59128983 2266254 0.03832729543141305 0.3708779667209533 chr20 63025520 2948883 0.046788713524299363 0.2462932068072092 chr21 48129895 1257714 0.026131658920095297 0.20371747320679479 chr22 51304566 791577 0.015428977607957936 0.13845102284975885 chrMT 16571 24635 1.4866332749984914 1.5153093799787574 chrX 155270560 6310094 0.040639345926233535 0.24881257887114885 chrY 59373566 336899 0.005674225462556855 0.17100577988680382