BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240264.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 = 2,029,991 number of mapped reads = 1,308,275 (64.45%) number of supplementary alignments = 5,816 (0.29%) number of secondary alignments = 0 number of mapped bases = 81,726,578 bp number of sequenced bases = 81,680,218 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 77,388 duplication rate = 4.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8003 >>>>>>> ACTG content number of A's = 23,078,652 bp (28.25%) number of C's = 14,213,172 bp (17.4%) number of T's = 26,290,521 bp (32.19%) number of G's = 18,077,847 bp (22.13%) number of N's = 20,026 bp (0.02%) GC percentage = 39.53% >>>>>>> Mismatches and indels general error rate = 0.0093 number of mismatches = 747,012 number of insertions = 6,417 mapped reads with insertion percentage = 0.48% number of deletions = 26,971 mapped reads with deletion percentage = 2.02% homopolymer indels = 48.76% >>>>>>> Coverage mean coverageData = 0.0264X std coverageData = 0.2984X There is a 2.15% of reference with a coverageData >= 1X There is a 0.35% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% 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 5717943 0.022940536625583773 0.40292726999589706 chr2 243199373 7298008 0.03000833394418332 0.3901058538945135 chr3 198022430 5814255 0.029361598077551114 0.20467544623415124 chr4 191154276 5288135 0.02766422551803131 0.20290074901612262 chr5 180915260 4230445 0.02338357195517946 0.2827282637686588 chr6 171115067 5118177 0.029910732524798648 0.288709065291943 chr7 159138663 5189996 0.032613042626856804 0.4845482313708552 chr8 146364022 5524902 0.03774767818282556 0.4504136731077829 chr9 141213431 2599597 0.01840899255538944 0.24455712244524844 chr10 135534747 4000613 0.029517249919682957 0.2483245464489833 chr11 135006516 4171588 0.03089916045237402 0.31563713154349887 chr12 133851895 4086092 0.030526964149442934 0.21201664358950156 chr13 115169878 1395912 0.012120460872590314 0.1304202733758804 chr14 107349540 3490013 0.03251074014849062 0.22228311976863419 chr15 102531392 1618103 0.015781537424167616 0.16051232159840945 chr16 90354753 2239982 0.024790970321173916 0.19309755907949352 chr17 81195210 1732260 0.021334509757410566 0.20130939944774878 chr18 78077248 2040555 0.02613507842899381 0.4131021516134966 chr19 59128983 1259254 0.021296730234646517 0.29740092746818814 chr20 63025520 1578017 0.025037746614387315 0.1932638006611613 chr21 48129895 1902540 0.039529278009021215 0.24635091468010692 chr22 51304566 458830 0.008943258578583434 0.10784800178459121 chrMT 16571 18120 1.0934765554281576 1.6107496825673104 chrX 155270560 4783272 0.030806045911085784 0.2330613117767802 chrY 59373566 169969 0.0028627049283177636 0.06849082512574849