BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240016.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 = 1,706,041 number of mapped reads = 1,401,984 (82.18%) number of supplementary alignments = 8,066 (0.47%) number of secondary alignments = 0 number of mapped bases = 88,474,472 bp number of sequenced bases = 88,431,442 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 121,628 duplication rate = 7.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8552 >>>>>>> ACTG content number of A's = 24,403,539 bp (27.6%) number of C's = 15,621,041 bp (17.66%) number of T's = 28,588,650 bp (32.33%) number of G's = 19,756,612 bp (22.34%) number of N's = 61,600 bp (0.07%) GC percentage = 40.01% >>>>>>> Mismatches and indels general error rate = 0.0094 number of mismatches = 819,158 number of insertions = 6,273 mapped reads with insertion percentage = 0.44% number of deletions = 25,415 mapped reads with deletion percentage = 1.79% homopolymer indels = 48.52% >>>>>>> Coverage mean coverageData = 0.0286X std coverageData = 0.304X There is a 2.08% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.15% of reference with a coverageData >= 3X There is a 0.04% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 6210305 0.024915905826369034 0.4507482754443915 chr2 243199373 9841150 0.04046535925896486 0.37701696262806195 chr3 198022430 6706521 0.03386748157771824 0.24251585506765042 chr4 191154276 6234760 0.032616377360033526 0.24154788628010349 chr5 180915260 4583138 0.02533306477297714 0.22949533786072945 chr6 171115067 4427240 0.025872882368681186 0.23006110836738286 chr7 159138663 5816116 0.036547473067559955 0.5116715140620414 chr8 146364022 4686065 0.032016508811161255 0.43473924886064375 chr9 141213431 4025893 0.02850927827112989 0.26780938326304654 chr10 135534747 4007833 0.02957052039208809 0.2736353481567658 chr11 135006516 3659320 0.02710476581737729 0.24614215650422694 chr12 133851895 4073148 0.0304302602514518 0.23021619777921729 chr13 115169878 2137508 0.018559609831313707 0.18017929273569094 chr14 107349540 2929810 0.02729224550007387 0.22590897069179636 chr15 102531392 1893177 0.018464364552858114 0.17641506189846523 chr16 90354753 2560645 0.02833990371264697 0.22192087400128577 chr17 81195210 2531143 0.031173550755026067 0.23911107211558852 chr18 78077248 1994241 0.025541896661111826 0.37300129642440727 chr19 59128983 1608870 0.027209498935572764 0.3373716599146043 chr20 63025520 2008081 0.03186139519356603 0.23611621845477324 chr21 48129895 1520058 0.03158240839710953 0.23875751925597963 chr22 51304566 890826 0.017363483788168096 0.1662053137426667 chrMT 16571 28203 1.7019491883410778 2.098891008000724 chrX 155270560 3922975 0.025265414126155017 0.21622571589748155 chrY 59373566 177446 0.0029886363908140537 0.07050216090592264