BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818978.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 = 719,578 number of mapped reads = 656,887 (91.29%) number of supplementary alignments = 10,904 (1.52%) number of secondary alignments = 0 number of mapped bases = 60,731,015 bp number of sequenced bases = 60,693,511 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 192,288 duplication rate = 24.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0413 >>>>>>> ACTG content number of A's = 17,440,143 bp (28.73%) number of C's = 12,334,989 bp (20.32%) number of T's = 17,595,777 bp (28.99%) number of G's = 13,319,711 bp (21.95%) number of N's = 2,891 bp (0%) GC percentage = 42.27% >>>>>>> Mismatches and indels general error rate = 0.0067 number of mismatches = 384,396 number of insertions = 9,539 mapped reads with insertion percentage = 1.41% number of deletions = 20,141 mapped reads with deletion percentage = 3% homopolymer indels = 42.56% >>>>>>> Coverage mean coverageData = 0.0196X std coverageData = 0.2757X There is a 1.26% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.06% 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% 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 6033808 0.024207795253597383 0.45548171511232954 chr2 243199373 5071048 0.020851402441732447 0.36869683611426485 chr3 198022430 3350086 0.0169177097766147 0.1903462626017862 chr4 191154276 3430842 0.01794802644121861 0.20559766795822343 chr5 180915260 3246199 0.01794320169564469 0.19799812829438324 chr6 171115067 2467485 0.014420033508796745 0.1890363293720987 chr7 159138663 3118248 0.019594534359007404 0.28795797766087344 chr8 146364022 4787618 0.03271034735571833 0.2850934255238679 chr9 141213431 2705438 0.01915850341459376 0.2652871482134431 chr10 135534747 3307338 0.024402140950615415 0.3167012070346087 chr11 135006516 1977852 0.014650048446550535 0.19567060088197474 chr12 133851895 2896301 0.021638102321973104 0.2184393995105878 chr13 115169878 1255921 0.010904943391535069 0.15112940161434418 chr14 107349540 1477381 0.013762341226613546 0.17780812671836108 chr15 102531392 1490267 0.014534738785171277 0.17571410850563754 chr16 90354753 1991492 0.02204081062564578 0.31534950550479207 chr17 81195210 2259604 0.027829277121150374 0.2615007144125176 chr18 78077248 1536063 0.019673631427173252 0.30725210176579876 chr19 59128983 1339939 0.022661289472879993 0.4160793698087167 chr20 63025520 1808427 0.028693567304165044 0.2580870839857662 chr21 48129895 863332 0.017937541729521746 0.20527946949867537 chr22 51304566 511536 0.009970574548861792 0.16222852171383823 chrMT 16571 8141 0.49127994689517834 1.0209748155932437 chrX 155270560 3587768 0.02310655670978452 0.2377763324906915 chrY 59373566 208881 0.0035180807566788223 0.26478432804198027