BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124805.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 589,044 number of mapped reads = 588,173 (99.85%) number of supplementary alignments = 268,155 (45.52%) number of secondary alignments = 0 number of mapped bases = 88,741,132 bp number of sequenced bases = 88,698,352 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 855,088 duplication rate = 30.32% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.7567 >>>>>>> ACTG content number of A's = 27,120,031 bp (30.58%) number of C's = 15,190,818 bp (17.13%) number of T's = 28,119,610 bp (31.7%) number of G's = 18,267,893 bp (20.6%) number of N's = 0 bp (0%) GC percentage = 37.72% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 913,996 number of insertions = 20,936 mapped reads with insertion percentage = 3.52% number of deletions = 40,484 mapped reads with deletion percentage = 6.71% homopolymer indels = 86.49% >>>>>>> Coverage mean coverageData = 0.0287X std coverageData = 68.0972X There is a 0% of reference with a coverageData >= 1X There is a 0% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 120994 4.8543108745153335E-4 0.42084275400428517 chr2 243199373 13303 5.4699976549692835E-5 0.046810510402803734 chr3 198022430 12372 6.247777082626448E-5 0.06952765596012431 chr4 191154276 5706 2.9850234686876687E-5 0.005611773807062202 chr5 180915260 5197 2.8726156102033625E-5 0.00538121588793915 chr6 171115067 4561 2.665457858249268E-5 0.005162738431872494 chr7 159138663 11351 7.132773259506396E-5 0.07405712139640837 chr8 146364022 60059592 0.41034395734219437 281.07216883889544 chr9 141213431 2366 1.675478021633792E-5 0.004092360963013124 chr10 135534747 28448832 0.2099006537415826 143.53594859966398 chr11 135006516 3946 2.9228218880931645E-5 0.0055901242961270215 chr12 133851895 4030 3.0107903963556138E-5 0.005484941749512676 chr13 115169878 3175 2.7567972243575702E-5 0.005250448766580061 chr14 107349540 21994 2.048821075525801E-4 0.2764847315794894 chr15 102531392 5373 5.240346293162586E-5 0.016620013647967277 chr16 90354753 2422 2.6805452060723356E-5 0.005315504369949858 chr17 81195210 2199 2.708287841117721E-5 0.00522884157448174 chr18 78077248 2049 2.6243240540445278E-5 0.0051089796549006194 chr19 59128983 1412 2.3879998071335E-5 0.004876264921408369 chr20 63025520 1427 2.2641621996930766E-5 0.004753263273101949 chr21 48129895 1338 2.779976976887234E-5 0.005280350875791821 chr22 51304566 1205 2.3487188255329945E-5 0.0048463013326987625 chrMT 16571 0 0.0 0.0 chrX 155270560 3899 2.5111006233248595E-5 0.01539496743604889 chrY 59373566 2389 4.0236761255000245E-5 0.006483617231246524