BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3124878.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP068920/SRP068920.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 = 4,278,302 number of mapped reads = 4,225,793 (98.77%) number of supplementary alignments = 40,761 (0.95%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 2,116,764 number of mapped paired reads (second in pair) = 2,109,029 number of mapped paired reads (both in pair) = 4,209,942 number of mapped paired reads (singletons) = 15,851 number of mapped bases = 569,426,551 bp number of sequenced bases = 569,085,798 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 613,494 duplication rate = 14.59% >>>>>>> Insert size mean insert size = 72,736.1732 std insert size = 2,570,803.3326 median insert size = 166 >>>>>>> Mapping quality mean mapping quality = 53.835 >>>>>>> ACTG content number of A's = 165,137,400 bp (29.02%) number of C's = 117,782,103 bp (20.7%) number of T's = 164,937,002 bp (28.98%) number of G's = 121,203,562 bp (21.3%) number of N's = 25,731 bp (0%) GC percentage = 41.99% >>>>>>> Mismatches and indels general error rate = 0.0131 number of mismatches = 7,275,480 number of insertions = 85,995 mapped reads with insertion percentage = 1.97% number of deletions = 190,624 mapped reads with deletion percentage = 4.38% homopolymer indels = 47.21% >>>>>>> Coverage mean coverageData = 0.1839X std coverageData = 1.7817X There is a 9.62% of reference with a coverageData >= 1X There is a 5.78% of reference with a coverageData >= 2X There is a 1.25% of reference with a coverageData >= 3X There is a 0.64% of reference with a coverageData >= 4X There is a 0.22% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.05% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.03% of reference with a coverageData >= 10X There is a 0.02% of reference with a coverageData >= 11X There is a 0.02% of reference with a coverageData >= 12X There is a 0.02% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% 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 0.01% 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 47128159 0.18907940454038027 3.4570011393058686 chr2 243199373 47205187 0.19410077590948394 1.6144273259678432 chr3 198022430 43522343 0.21978491527449692 0.7388039340524993 chr4 191154276 24041872 0.12577208578896765 0.6241233377725518 chr5 180915260 27975218 0.15463161040146642 0.5659869171895817 chr6 171115067 40881127 0.2389101539492136 1.4728163055452634 chr7 159138663 51455842 0.32333966510702683 2.7071758817268305 chr8 146364022 34669427 0.23687123738646645 0.9818545811704569 chr9 141213431 18236364 0.1291404356572853 1.7692167442551525 chr10 135534747 19756620 0.14576793359122883 3.897329817675082 chr11 135006516 32194175 0.23846386051470286 1.5760661964118476 chr12 133851895 23393073 0.17476833630185065 0.5949057506481067 chr13 115169878 21588505 0.18744923043158906 0.668449568115582 chr14 107349540 15661809 0.1458954458491392 0.5840965351066844 chr15 102531392 18830964 0.18366047346748204 0.6339909012442807 chr16 90354753 11096302 0.12280817147494166 1.2467352996500531 chr17 81195210 15258609 0.18792498966379914 2.1437672734920366 chr18 78077248 16376333 0.20974526407488134 2.1222492128697867 chr19 59128983 11759443 0.1988778159773186 1.9255111400858975 chr20 63025520 15435125 0.2449027790647344 0.7448371645914406 chr21 48129895 8600244 0.17868819368918215 0.7249293635472006 chr22 51304566 3945872 0.07691073734061019 0.39473160701462207 chrMT 16571 11661 0.703699233600869 1.0663568093788265 chrX 155270560 15970355 0.10285500999030338 0.6311426739941971 chrY 59373566 4431922 0.07464469962946137 0.9916561011478185