BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6008756.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 = 1,212,035 number of mapped reads = 1,075,862 (88.76%) number of supplementary alignments = 11,013 (0.91%) number of secondary alignments = 0 number of mapped bases = 72,029,937 bp number of sequenced bases = 71,988,507 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 50,651 duplication rate = 3.89% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.7759 >>>>>>> ACTG content number of A's = 19,503,769 bp (27.09%) number of C's = 13,904,599 bp (19.32%) number of T's = 22,237,441 bp (30.89%) number of G's = 16,238,329 bp (22.56%) number of N's = 104,369 bp (0.14%) GC percentage = 41.87% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 615,653 number of insertions = 5,056 mapped reads with insertion percentage = 0.47% number of deletions = 23,294 mapped reads with deletion percentage = 2.14% homopolymer indels = 45.1% >>>>>>> Coverage mean coverageData = 0.0233X std coverageData = 0.2367X There is a 1.83% of reference with a coverageData >= 1X There is a 0.36% 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 4807302 0.01928702115450296 0.3313856828904148 chr2 243199373 6300709 0.025907587352209167 0.31923428630895656 chr3 198022430 1662380 0.00839490758698396 0.11080989158364866 chr4 191154276 6311223 0.033016384106416746 0.22608931562797535 chr5 180915260 4183723 0.023125318450195966 0.18625079726276944 chr6 171115067 5165147 0.030185226178826206 0.23137600440741823 chr7 159138663 4566302 0.028693856753088342 0.30527685383568687 chr8 146364022 3429143 0.023428865599224923 0.2836671578346359 chr9 141213431 2878845 0.020386481509680195 0.2038228949835262 chr10 135534747 2450419 0.018079636803394777 0.19457886741913427 chr11 135006516 4950361 0.0366675709193177 0.2645652315113258 chr12 133851895 1373297 0.010259824860903165 0.1239512987334631 chr13 115169878 4461972 0.03874252606223999 0.24252186527981198 chr14 107349540 2616788 0.024376331747672137 0.19770485026084886 chr15 102531392 1861409 0.018154527737222176 0.1652158022203136 chr16 90354753 3198439 0.03539868013362839 0.246216504304816 chr17 81195210 1992350 0.02453777753638423 0.20189886971899446 chr18 78077248 293312 0.003756689784967831 0.23817825800459558 chr19 59128983 1612948 0.02727846680535669 0.2850801578980939 chr20 63025520 1562505 0.024791624091320467 0.19837653218004514 chr21 48129895 903936 0.018781175400444983 0.17501338553145512 chr22 51304566 944002 0.018399960736438157 0.16773351120953642 chrMT 16571 17602 1.0622171263049907 1.4643229129801976 chrX 155270560 4297416 0.02767695305536349 0.20743460367536024 chrY 59373566 188407 0.0031732471652452204 0.081635088239833