BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234127.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 = 3,423,883 number of mapped reads = 2,947,015 (86.07%) number of supplementary alignments = 28,022 (0.82%) number of secondary alignments = 0 number of mapped bases = 203,600,340 bp number of sequenced bases = 203,541,763 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,045,831 duplication rate = 13.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.3671 >>>>>>> ACTG content number of A's = 44,575,002 bp (21.9%) number of C's = 33,150,763 bp (16.29%) number of T's = 47,919,452 bp (23.54%) number of G's = 77,855,566 bp (38.25%) number of N's = 40,980 bp (0.02%) GC percentage = 54.54% >>>>>>> Mismatches and indels general error rate = 0.0055 number of mismatches = 1,101,956 number of insertions = 11,804 mapped reads with insertion percentage = 0.4% number of deletions = 34,770 mapped reads with deletion percentage = 1.17% homopolymer indels = 46.15% >>>>>>> Coverage mean coverageData = 0.0658X std coverageData = 83.2341X There is a 1.25% of reference with a coverageData >= 1X There is a 0.83% of reference with a coverageData >= 2X There is a 0.64% of reference with a coverageData >= 3X There is a 0.5% of reference with a coverageData >= 4X There is a 0.39% of reference with a coverageData >= 5X There is a 0.31% of reference with a coverageData >= 6X There is a 0.24% of reference with a coverageData >= 7X There is a 0.19% of reference with a coverageData >= 8X There is a 0.15% of reference with a coverageData >= 9X There is a 0.12% of reference with a coverageData >= 10X There is a 0.1% of reference with a coverageData >= 11X There is a 0.08% of reference with a coverageData >= 12X There is a 0.06% of reference with a coverageData >= 13X There is a 0.05% of reference with a coverageData >= 14X There is a 0.04% of reference with a coverageData >= 15X There is a 0.04% of reference with a coverageData >= 16X There is a 0.03% of reference with a coverageData >= 17X There is a 0.03% of reference with a coverageData >= 18X There is a 0.02% of reference with a coverageData >= 19X There is a 0.02% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% 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 9837259 0.039467339983076714 0.7024673755776615 chr2 243199373 51231753 0.21065742221300876 296.949757091679 chr3 198022430 25900450 0.1307955366470354 1.0911183335469217 chr4 191154276 14047660 0.0734885993342885 0.8123035635644613 chr5 180915260 5670432 0.031343027669418266 0.5188300267323436 chr6 171115067 12700758 0.07422349313050265 0.882412234620974 chr7 159138663 4976043 0.03126859875654479 0.6541169614585503 chr8 146364022 7394953 0.050524390481699114 0.701357358780933 chr9 141213431 7081111 0.05014474154374168 0.7187184305576204 chr10 135534747 5290722 0.03903590862939376 0.605151414801661 chr11 135006516 4349950 0.03222029668553183 0.6573423901360204 chr12 133851895 4489121 0.033537971203171986 0.6446702854928478 chr13 115169878 3255922 0.028270603881337793 0.5180913213987909 chr14 107349540 3246872 0.030245793321517726 0.6048350895594028 chr15 102531392 2663298 0.02597543979506296 0.613214616194519 chr16 90354753 3170604 0.03509061664968527 0.5947750917481279 chr17 81195210 4011986 0.04941160937942029 0.6646275029906021 chr18 78077248 2643602 0.03385880096593569 0.6781278357406899 chr19 59128983 19616337 0.3317550210528735 1.8572295874760627 chr20 63025520 3510832 0.055704927146971575 0.713794560828751 chr21 48129895 1265210 0.026287404117544825 0.5020784446477673 chr22 51304566 1336892 0.026057953594227853 0.48978689353192234 chrMT 16571 195406 11.79204634602619 14.166412213695876 chrX 155270560 5049951 0.03252355758876634 0.5368203342428238 chrY 59373566 663216 0.011170223462744346 0.26578778182428153