BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6063580.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 = 2,728,387 number of mapped reads = 2,402,664 (88.06%) number of supplementary alignments = 16,911 (0.62%) number of secondary alignments = 0 number of mapped bases = 159,115,640 bp number of sequenced bases = 159,042,646 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 326,364 duplication rate = 10.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.426 >>>>>>> ACTG content number of A's = 44,468,406 bp (27.96%) number of C's = 29,313,139 bp (18.43%) number of T's = 50,586,493 bp (31.81%) number of G's = 34,670,163 bp (21.8%) number of N's = 4,445 bp (0%) GC percentage = 40.23% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 1,195,898 number of insertions = 11,933 mapped reads with insertion percentage = 0.49% number of deletions = 41,101 mapped reads with deletion percentage = 1.69% homopolymer indels = 47.9% >>>>>>> Coverage mean coverageData = 0.0514X std coverageData = 0.5632X There is a 2.43% of reference with a coverageData >= 1X There is a 1.2% of reference with a coverageData >= 2X There is a 0.63% of reference with a coverageData >= 3X There is a 0.34% of reference with a coverageData >= 4X There is a 0.19% of reference with a coverageData >= 5X There is a 0.11% of reference with a coverageData >= 6X There is a 0.06% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% 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 21588624 0.08661412322017846 0.6643498384126181 chr2 243199373 10005260 0.04114015540656842 0.5686103665513972 chr3 198022430 5059898 0.02555214578469722 0.290703784513251 chr4 191154276 8874702 0.046426908075025225 0.4488995069165361 chr5 180915260 5128039 0.02834497764312419 0.3330392295419035 chr6 171115067 4289187 0.02506609777384478 0.29081214613183004 chr7 159138663 5927494 0.037247353272032956 0.5990610360165461 chr8 146364022 4511276 0.030822301398631968 0.40974822554776963 chr9 141213431 21522656 0.1524122446964694 0.9912130157979834 chr10 135534747 4771300 0.03520351869620563 0.5273334737711317 chr11 135006516 4660997 0.03452423733384839 0.4362332839966841 chr12 133851895 5009427 0.03742514814601616 0.4164654944012622 chr13 115169878 2135205 0.018539613283257973 0.24007072452777814 chr14 107349540 2653403 0.024717413786775427 0.47257705334068745 chr15 102531392 2570552 0.025070877804916566 0.28163858959193533 chr16 90354753 2353421 0.02604645491089993 0.44499547420842867 chr17 81195210 2403992 0.02960755936218405 0.31715203218487076 chr18 78077248 2216605 0.02838989663160259 1.3446577307495973 chr19 59128983 2619225 0.04429680449602862 0.4916468951988406 chr20 63025520 3572579 0.05668464139605671 0.4506574073025459 chr21 48129895 1399053 0.029068274510052432 0.5146473766756469 chr22 51304566 827812 0.016135250028233353 0.22316286026461105 chrMT 16571 184730 11.147788304869954 8.766312270382866 chrX 155270560 34380639 0.22142406776918946 0.9289524219754257 chrY 59373566 449564 0.007571787081139779 0.244453891832036