BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094158.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 28,440 number of mapped reads = 756 (2.66%) number of supplementary alignments = 24 (0.08%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 282 number of mapped paired reads (second in pair) = 474 number of mapped paired reads (both in pair) = 514 number of mapped paired reads (singletons) = 242 number of mapped bases = 59,074 bp number of sequenced bases = 58,686 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 484 duplication rate = 21.62% >>>>>>> Insert size mean insert size = 221.2429 std insert size = 1,832.2489 median insert size = 36 >>>>>>> Mapping quality mean mapping quality = 8.1643 >>>>>>> ACTG content number of A's = 11,268 bp (19.2%) number of C's = 8,608 bp (14.67%) number of T's = 9,677 bp (16.49%) number of G's = 29,133 bp (49.64%) number of N's = 0 bp (0%) GC percentage = 64.31% >>>>>>> Mismatches and indels general error rate = 0.0293 number of mismatches = 1,394 number of insertions = 67 mapped reads with insertion percentage = 6.08% number of deletions = 65 mapped reads with deletion percentage = 8.6% homopolymer indels = 46.97% >>>>>>> Coverage mean coverageData = 0X std coverageData = 0.0274X 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 466 1.869604168408471E-6 0.0015280693119256803 chr2 243199373 21661 8.906684146755592E-5 0.08519319750444344 chr3 198022430 985 4.974183985117242E-6 0.002757748062338699 chr4 191154276 861 4.504215223519248E-6 0.0021985840230391695 chr5 180915260 287 1.5863780645148453E-6 0.0013361750398793585 chr6 171115067 531 3.1031750114675756E-6 0.002029784468866075 chr7 159138663 1331 8.363775181396366E-6 0.0037759690516949843 chr8 146364022 697 4.76209925414594E-6 0.002838174695409333 chr9 141213431 780 5.52355391747404E-6 0.0026330092827314615 chr10 135534747 278 2.0511345330507753E-6 0.0017853207888294893 chr11 135006516 1589 1.1769802281246928E-5 0.004532065011480506 chr12 133851895 91 6.798558959512676E-7 8.2453346429798E-4 chr13 115169878 258 2.24016908310001E-6 0.002100207298392846 chr14 107349540 412 3.837929813206466E-6 0.00224282893404959 chr15 102531392 85 8.290143959032566E-7 9.105018993052062E-4 chr16 90354753 68 7.525890751978482E-7 8.675185927733953E-4 chr17 81195210 662 8.153190317507647E-6 0.0036571993062160142 chr18 78077248 288 3.688654600121152E-6 0.002716117743042364 chr19 59128983 226 3.822152665808576E-6 0.002199288260594764 chr20 63025520 638 1.0122883555740595E-5 0.003841331145243098 chr21 48129895 291 6.0461382681179755E-6 0.002915098779455542 chr22 51304566 0 0.0 0.0 chrMT 16571 5553 0.33510349405588075 1.6458248522724122 chrX 155270560 20912 1.3468103676575908E-4 0.05627818660410452 chrY 59373566 124 2.0884714925157096E-6 0.0020437560087540403