BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238532.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 = 4,160,206 number of mapped reads = 3,179,434 (76.42%) number of supplementary alignments = 25,870 (0.62%) number of secondary alignments = 0 number of mapped bases = 191,956,145 bp number of sequenced bases = 191,858,002 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 1,417,579 duplication rate = 22.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.922 >>>>>>> ACTG content number of A's = 47,441,967 bp (24.73%) number of C's = 32,656,051 bp (17.02%) number of T's = 65,796,158 bp (34.29%) number of G's = 45,959,595 bp (23.96%) number of N's = 4,231 bp (0%) GC percentage = 40.98% >>>>>>> Mismatches and indels general error rate = 0.0062 number of mismatches = 1,155,047 number of insertions = 13,264 mapped reads with insertion percentage = 0.41% number of deletions = 58,623 mapped reads with deletion percentage = 1.82% homopolymer indels = 41.99% >>>>>>> Coverage mean coverageData = 0.062X std coverageData = 1.245X There is a 1.47% of reference with a coverageData >= 1X There is a 0.85% of reference with a coverageData >= 2X There is a 0.66% of reference with a coverageData >= 3X There is a 0.54% of reference with a coverageData >= 4X There is a 0.44% of reference with a coverageData >= 5X There is a 0.36% of reference with a coverageData >= 6X There is a 0.3% of reference with a coverageData >= 7X There is a 0.24% of reference with a coverageData >= 8X There is a 0.2% of reference with a coverageData >= 9X There is a 0.17% of reference with a coverageData >= 10X There is a 0.14% of reference with a coverageData >= 11X There is a 0.11% of reference with a coverageData >= 12X There is a 0.1% of reference with a coverageData >= 13X There is a 0.08% of reference with a coverageData >= 14X There is a 0.07% of reference with a coverageData >= 15X There is a 0.06% of reference with a coverageData >= 16X There is a 0.05% of reference with a coverageData >= 17X There is a 0.04% of reference with a coverageData >= 18X There is a 0.03% of reference with a coverageData >= 19X There is a 0.03% of reference with a coverageData >= 20X There is a 0.02% of reference with a coverageData >= 21X There is a 0.02% of reference with a coverageData >= 22X There is a 0.02% of reference with a coverageData >= 23X There is a 0.02% 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 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% 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 17337994 0.06956048466575335 1.4739512805265838 chr2 243199373 18289535 0.07520387398367183 2.5099777383396717 chr3 198022430 12006579 0.0606324192668477 0.8051466316665679 chr4 191154276 11376936 0.05951703638583528 0.7764024276459229 chr5 180915260 9704293 0.05363999145235178 0.7333907119253243 chr6 171115067 10389638 0.06071725992428241 1.095270683780796 chr7 159138663 12128126 0.07621105877960029 1.1674858386514084 chr8 146364022 10283865 0.07026224655127337 0.9885986225931336 chr9 141213431 8667611 0.06137950858229625 0.8817551305299886 chr10 135534747 10365329 0.07647728150479374 1.061643847498651 chr11 135006516 9135864 0.06766980047096394 0.8466010469658147 chr12 133851895 9542267 0.0712897415460573 0.864541462586406 chr13 115169878 5705680 0.04954142610101575 0.9246123378972768 chr14 107349540 4769388 0.04442858348531349 0.706194400251447 chr15 102531392 6052742 0.05903306179633258 0.9359526983025541 chr16 90354753 5028683 0.055654880712252074 0.7818520089006163 chr17 81195210 4436949 0.0546454526073644 0.7502117959812633 chr18 78077248 4910923 0.06289825942635684 3.108542867291045 chr19 59128983 3792234 0.0641349437719908 1.077352250074148 chr20 63025520 4320625 0.06855357956586475 0.8646941212214985 chr21 48129895 1796877 0.03733390650447087 0.5851465818069947 chr22 51304566 1416766 0.027614813075311856 0.5248209327111161 chrMT 16571 89197 5.3827167943998555 8.352496338676941 chrX 155270560 9870770 0.06357142010694107 0.8109007208513376 chrY 59373566 537274 0.009049043811853915 0.4347044154743291