BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6068956.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 = 2,360,808 number of mapped reads = 1,990,263 (84.3%) number of supplementary alignments = 11,318 (0.48%) number of secondary alignments = 0 number of mapped bases = 129,042,410 bp number of sequenced bases = 128,983,393 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 81,036 duplication rate = 3.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.3138 >>>>>>> ACTG content number of A's = 34,674,329 bp (26.88%) number of C's = 22,045,569 bp (17.09%) number of T's = 42,770,991 bp (33.16%) number of G's = 29,181,342 bp (22.62%) number of N's = 311,162 bp (0.24%) GC percentage = 39.72% >>>>>>> Mismatches and indels general error rate = 0.0095 number of mismatches = 1,206,349 number of insertions = 11,071 mapped reads with insertion percentage = 0.55% number of deletions = 36,518 mapped reads with deletion percentage = 1.82% homopolymer indels = 48.79% >>>>>>> Coverage mean coverageData = 0.0417X std coverageData = 0.3734X There is a 3.62% of reference with a coverageData >= 1X There is a 0.4% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.01% 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 15023046 0.060272852840755814 0.7125581694985121 chr2 243199373 10106658 0.04155708904726493 0.31188744414235586 chr3 198022430 7266333 0.036694494659014136 0.2164154158577501 chr4 191154276 6605708 0.03455694603452135 0.2251155716675376 chr5 180915260 7327955 0.04050490268206231 0.22424789169186313 chr6 171115067 9882809 0.057755340738054356 0.34997433879742007 chr7 159138663 9886204 0.06212320635118067 0.5728362140830936 chr8 146364022 9543237 0.06520206857939446 0.6655331410598851 chr9 141213431 4799046 0.03398434529927964 0.27884924581725146 chr10 135534747 5400968 0.03984932365720209 0.33350104427298705 chr11 135006516 5110385 0.037852876671523025 0.29453286748563307 chr12 133851895 5944968 0.044414522483973796 0.23734921322256106 chr13 115169878 3493678 0.030334997836847583 0.1921538917810698 chr14 107349540 3815703 0.03554466092728483 0.2183260838109055 chr15 102531392 3064822 0.029891547751541302 0.19136754168834566 chr16 90354753 2593940 0.028708395672333915 0.20580756607035094 chr17 81195210 3428719 0.04222809448981042 0.2478683146170368 chr18 78077248 1871055 0.02396415150288084 0.43316211983730984 chr19 59128983 2085118 0.03526389080630729 0.45333209663679697 chr20 63025520 1518808 0.02409830176728411 0.1837913710682703 chr21 48129895 1422532 0.029556100215884534 0.20088924746381864 chr22 51304566 665944 0.012980209207889996 0.1285822145384545 chrMT 16571 211589 12.76863194737795 6.348179954485549 chrX 155270560 7675195 0.049431102715157334 0.27547341300328004 chrY 59373566 297990 0.005018900161731906 0.11377983092253453