BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008767.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 = 1,822,612 number of mapped reads = 1,618,269 (88.79%) number of supplementary alignments = 11,866 (0.65%) number of secondary alignments = 0 number of mapped bases = 102,297,102 bp number of sequenced bases = 102,245,724 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 96,940 duplication rate = 4.94% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.8804 >>>>>>> ACTG content number of A's = 26,642,324 bp (26.06%) number of C's = 17,931,722 bp (17.54%) number of T's = 33,132,564 bp (32.4%) number of G's = 24,520,953 bp (23.98%) number of N's = 18,161 bp (0.02%) GC percentage = 41.52% >>>>>>> Mismatches and indels general error rate = 0.0075 number of mismatches = 756,299 number of insertions = 7,746 mapped reads with insertion percentage = 0.48% number of deletions = 31,280 mapped reads with deletion percentage = 1.91% homopolymer indels = 45.82% >>>>>>> Coverage mean coverageData = 0.033X std coverageData = 0.3391X There is a 2.72% of reference with a coverageData >= 1X There is a 0.42% of reference with a coverageData >= 2X There is a 0.08% 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 3341911 0.013407834197532451 0.6064897728260511 chr2 243199373 11739571 0.04827138678519537 0.5082134996975091 chr3 198022430 5936649 0.029979679574682526 0.20355284560420692 chr4 191154276 9577875 0.050105470829226964 0.26678814354462393 chr5 180915260 2724094 0.015057292568907676 0.14949289114033026 chr6 171115067 4959816 0.028985267556830632 0.24930140428821554 chr7 159138663 6864300 0.04313408112521343 0.5153951330626143 chr8 146364022 4888707 0.03340101572229274 0.29069193108857144 chr9 141213431 1454716 0.010301541359759187 0.2649097036778923 chr10 135534747 8900713 0.06567107842832362 0.35642995965542595 chr11 135006516 2647142 0.0196075128699714 0.2010749971652071 chr12 133851895 3391551 0.025338087294169424 0.19606422833930337 chr13 115169878 1900385 0.016500712104600822 0.15063277957606672 chr14 107349540 6387857 0.05950521073495052 0.2877017168139267 chr15 102531392 3671756 0.03581104214404892 0.21980566594166878 chr16 90354753 5547367 0.061395408828133255 0.3546057794645752 chr17 81195210 2052923 0.025283794450436176 0.18926935795453517 chr18 78077248 1457210 0.018663695728619943 0.3544645967302894 chr19 59128983 3909678 0.06612117783253603 0.4861738444851949 chr20 63025520 4166072 0.0661013506909582 0.3057724689355912 chr21 48129895 1159529 0.02409165862506037 0.1881672673493756 chr22 51304566 756392 0.014743171202344836 0.13937362580916277 chrMT 16571 111931 6.75463158529962 4.345542009244207 chrX 155270560 4447741 0.028645101814535865 0.2085028448383339 chrY 59373566 301216 0.005073234105561387 0.11488601490503436