BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238486.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 = 2,845,091 number of mapped reads = 2,318,338 (81.49%) number of supplementary alignments = 24,187 (0.85%) number of secondary alignments = 0 number of mapped bases = 137,330,366 bp number of sequenced bases = 137,244,804 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 991,737 duplication rate = 23.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.5941 >>>>>>> ACTG content number of A's = 33,462,645 bp (24.38%) number of C's = 23,490,923 bp (17.12%) number of T's = 47,474,477 bp (34.59%) number of G's = 32,814,015 bp (23.91%) number of N's = 2,744 bp (0%) GC percentage = 41.03% >>>>>>> Mismatches and indels general error rate = 0.0072 number of mismatches = 972,012 number of insertions = 8,835 mapped reads with insertion percentage = 0.38% number of deletions = 52,328 mapped reads with deletion percentage = 2.23% homopolymer indels = 39.26% >>>>>>> Coverage mean coverageData = 0.0444X std coverageData = 1.1075X There is a 1.28% of reference with a coverageData >= 1X There is a 0.67% of reference with a coverageData >= 2X There is a 0.51% of reference with a coverageData >= 3X There is a 0.4% of reference with a coverageData >= 4X There is a 0.31% of reference with a coverageData >= 5X There is a 0.25% of reference with a coverageData >= 6X There is a 0.19% of reference with a coverageData >= 7X There is a 0.15% of reference with a coverageData >= 8X There is a 0.12% of reference with a coverageData >= 9X There is a 0.09% of reference with a coverageData >= 10X There is a 0.07% of reference with a coverageData >= 11X There is a 0.06% of reference with a coverageData >= 12X There is a 0.05% of reference with a coverageData >= 13X There is a 0.04% of reference with a coverageData >= 14X There is a 0.03% of reference with a coverageData >= 15X There is a 0.02% of reference with a coverageData >= 16X There is a 0.02% of reference with a coverageData >= 17X There is a 0.02% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% 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 7094633 0.02846385285435257 0.5490041153010075 chr2 243199373 6592919 0.027109111831468413 2.511725692181805 chr3 198022430 7120184 0.03595645200394723 0.5652098615092445 chr4 191154276 6003911 0.03140871931109718 0.48758964090401213 chr5 180915260 4966008 0.027449359440436367 0.48049112942731786 chr6 171115067 7189979 0.04201838637622717 1.0321677573257826 chr7 159138663 8657457 0.05440197144297989 0.8946110219174431 chr8 146364022 6163734 0.04211235736607457 0.9085336653747431 chr9 141213431 4444101 0.03147080960025679 0.5767948383355835 chr10 135534747 8499564 0.06271132818804022 0.7384946581286399 chr11 135006516 18003125 0.13335004511930373 1.5743660251696345 chr12 133851895 4010875 0.0299650221612477 0.49837928600430786 chr13 115169878 1706958 0.01482121913856677 0.7149294606900564 chr14 107349540 8128709 0.07572188013101873 0.8143950113744715 chr15 102531392 6351879 0.06195057802394802 0.9249842013894294 chr16 90354753 7893166 0.08735750735769263 0.8746832503159332 chr17 81195210 1965138 0.02420263461354432 0.6266752799021107 chr18 78077248 6863882 0.08791142331246102 2.866473240956361 chr19 59128983 3331733 0.05634686799872746 0.7531582762076213 chr20 63025520 2752594 0.04367427670569001 0.6000375266099586 chr21 48129895 1580481 0.03283782356059576 0.5065224508702197 chr22 51304566 955285 0.018619882682566695 0.3715883758586118 chrMT 16571 155339 9.374147607265705 10.509461099961344 chrX 155270560 6521131 0.04199850248495272 0.6469392483551218 chrY 59373566 377581 0.0063594125372223725 0.43944323244459743