BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237307.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,722,167 number of mapped reads = 2,396,183 (88.02%) number of supplementary alignments = 29,353 (1.08%) number of secondary alignments = 0 number of mapped bases = 146,343,107 bp number of sequenced bases = 146,255,079 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 618,144 duplication rate = 19.2% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.2775 >>>>>>> ACTG content number of A's = 37,062,365 bp (25.34%) number of C's = 25,975,373 bp (17.76%) number of T's = 48,126,490 bp (32.91%) number of G's = 35,075,447 bp (23.98%) number of N's = 15,404 bp (0.01%) GC percentage = 41.74% >>>>>>> Mismatches and indels general error rate = 0.007 number of mismatches = 984,920 number of insertions = 12,810 mapped reads with insertion percentage = 0.53% number of deletions = 49,683 mapped reads with deletion percentage = 2.05% homopolymer indels = 41.16% >>>>>>> Coverage mean coverageData = 0.0473X std coverageData = 0.6826X There is a 2.37% of reference with a coverageData >= 1X There is a 1.1% of reference with a coverageData >= 2X There is a 0.55% of reference with a coverageData >= 3X There is a 0.28% of reference with a coverageData >= 4X There is a 0.14% of reference with a coverageData >= 5X There is a 0.07% of reference with a coverageData >= 6X There is a 0.04% of reference with a coverageData >= 7X There is a 0.02% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% 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 10693942 0.04290437454918116 0.8393682843682208 chr2 243199373 13805758 0.05676724339252306 1.3765912280107313 chr3 198022430 7747759 0.03912566369375429 0.34290066716553913 chr4 191154276 6103121 0.031927724180232306 0.6200275806235095 chr5 180915260 7687285 0.042491081183533105 0.3592676583510327 chr6 171115067 13348884 0.07801115491483868 0.6543913920765431 chr7 159138663 8858861 0.055667559554650775 0.554699722298233 chr8 146364022 8141964 0.055628178897680194 0.7945402638931783 chr9 141213431 6889653 0.04878893566434201 0.5063592573324633 chr10 135534747 5597807 0.04130163757932864 0.9284504396234873 chr11 135006516 6786876 0.05027072915502834 0.45888617533902776 chr12 133851895 6955338 0.051962940083888985 0.41565971172208843 chr13 115169878 5424944 0.04710384428817403 0.4296200199227408 chr14 107349540 5072549 0.047252638437016124 0.3896297207551857 chr15 102531392 2694160 0.02627644029254962 0.3056983209356952 chr16 90354753 5602047 0.06200057898448353 0.4897507651588555 chr17 81195210 3639816 0.044827964605301224 0.4165431293191561 chr18 78077248 4499583 0.0576298872624199 1.088227303099904 chr19 59128983 4697518 0.07944526967426448 0.7113096627033829 chr20 63025520 2773918 0.0440126158419637 0.3989384000392449 chr21 48129895 3056200 0.06349899579045415 0.5649699451349807 chr22 51304566 996366 0.01942061063336936 0.23090600989181045 chrMT 16571 16337 0.9858789451451331 1.529987365703091 chrX 155270560 4633818 0.02984350671498834 0.32128094153104975 chrY 59373566 618603 0.010418828473263675 0.5261902835679662