BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549028.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 8,695,625 number of mapped reads = 7,680,270 (88.32%) number of secondary alignments = 0 number of mapped bases = 303,653,427 bp number of sequenced bases = 303,623,540 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 335,051 duplication rate = 3.07% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.3102 >>>>>>> ACTG content number of A's = 86,137,685 bp (28.37%) number of C's = 64,790,328 bp (21.34%) number of T's = 87,416,198 bp (28.79%) number of G's = 65,276,100 bp (21.5%) number of N's = 3,229 bp (0%) GC percentage = 42.84% >>>>>>> Mismatches and indels general error rate = 0.0031 number of mismatches = 927,248 number of insertions = 10,578 mapped reads with insertion percentage = 0.14% number of deletions = 23,372 mapped reads with deletion percentage = 0.3% homopolymer indels = 38.71% >>>>>>> Coverage mean coverageData = 0.0981X std coverageData = 0.9714X There is a 7.64% of reference with a coverageData >= 1X There is a 1.52% of reference with a coverageData >= 2X There is a 0.34% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.03% 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 0.01% 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 23996359 0.09627401891207324 1.003402281738895 chr2 243199373 25494604 0.10483005644919981 0.7448407577067946 chr3 198022430 20353789 0.10278527033528474 0.3948110070748831 chr4 191154276 19430301 0.10164722132608742 0.4063120733359517 chr5 180915260 18678434 0.10324410444978495 0.4058802572791527 chr6 171115067 17541115 0.10251063981408487 0.4439315067094002 chr7 159138663 17002471 0.10684060478753676 1.0350556108909224 chr8 146364022 15667280 0.10704324591462784 3.316435492797458 chr9 141213431 12797655 0.09062633001247594 0.7861576318486312 chr10 135534747 13910929 0.10263736280114205 0.5284077250408727 chr11 135006516 13801887 0.10223126563757856 0.8408413188635447 chr12 133851895 13885037 0.10373433263682968 0.42382993956519005 chr13 115169878 9658833 0.08386596536986868 0.3510394684560056 chr14 107349540 9272570 0.08637736128165989 0.49399822546492483 chr15 102531392 8683601 0.08469212043858723 0.3583594699685354 chr16 90354753 8556128 0.09469483027638845 0.44374635583767297 chr17 81195210 8312879 0.10238139663657499 0.4488620775609101 chr18 78077248 8058430 0.10321098919879963 1.414632510909421 chr19 59128983 6447738 0.10904530524396132 1.027343995265784 chr20 63025520 6170961 0.09791209973356825 0.4111488288599606 chr21 48129895 3821782 0.07940557526668196 0.43585525103691636 chr22 51304566 3465596 0.06754946528540949 0.3556400195425536 chrMT 16571 13624 0.8221591937722528 1.2621243069606567 chrX 155270560 17632285 0.11355845564027077 0.5588500092501676 chrY 59373566 999139 0.01682801063355366 0.20199698576077357