BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2094027.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 370,950 number of mapped reads = 335,617 (90.47%) number of supplementary alignments = 18,756 (5.06%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 168,711 number of mapped paired reads (second in pair) = 166,906 number of mapped paired reads (both in pair) = 331,210 number of mapped paired reads (singletons) = 4,407 number of mapped bases = 42,723,228 bp number of sequenced bases = 41,999,505 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 311,838 duplication rate = 45.89% >>>>>>> Insert size mean insert size = 555,868.5864 std insert size = 6,929,361.8366 median insert size = 164 >>>>>>> Mapping quality mean mapping quality = 43.8352 >>>>>>> ACTG content number of A's = 11,696,728 bp (27.85%) number of C's = 9,359,727 bp (22.29%) number of T's = 11,169,373 bp (26.59%) number of G's = 9,773,268 bp (23.27%) number of N's = 409 bp (0%) GC percentage = 45.56% >>>>>>> Mismatches and indels general error rate = 0.0333 number of mismatches = 1,355,511 number of insertions = 24,009 mapped reads with insertion percentage = 7.04% number of deletions = 106,027 mapped reads with deletion percentage = 30.5% homopolymer indels = 29.06% >>>>>>> Coverage mean coverageData = 0.0138X std coverageData = 4.621X There is a 0.03% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0.01% 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 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% 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 0.01% 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 0.01% of reference with a coverageData >= 26X There is a 0.01% 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 664912 0.0026676443064910156 0.8588807427314951 chr2 243199373 2115274 0.008697695121113656 2.6635365920578193 chr3 198022430 662824 0.0033472167774125385 1.239910918960626 chr4 191154276 572869 0.002996893462116432 0.7949866129037013 chr5 180915260 1167972 0.0064559064835105675 2.886382804977705 chr6 171115067 830726 0.004854779970953698 1.6541936494167373 chr7 159138663 811644 0.00510023136238112 1.7871603117088384 chr8 146364022 1035561 0.007075242848956419 2.3146593340140993 chr9 141213431 456483 0.003232574952449105 1.4837268582689178 chr10 135534747 837354 0.00617815002082086 1.655840593041001 chr11 135006516 1038182 0.007689865872844241 2.101639060737743 chr12 133851895 725433 0.005419669254589186 1.2226283482788942 chr13 115169878 783978 0.006807144486165037 1.6288670571852686 chr14 107349540 384133 0.0035783385750884447 0.6923167053039867 chr15 102531392 517995 0.0050520624941871465 1.5963050503072609 chr16 90354753 243109 0.002690605551209907 0.8458593337284519 chr17 81195210 1809225 0.02228241050180177 5.377122495215189 chr18 78077248 128301 0.0016432572008685553 0.4938571755120686 chr19 59128983 265657 0.004492838985578358 0.9559754979422614 chr20 63025520 153128 0.002429618986086906 0.5369278901670231 chr21 48129895 380840 0.007912753601477834 2.85036900231498 chr22 51304566 190699 0.003716998600085614 0.3786688302526659 chrMT 16571 5908737 356.57093717940984 1510.3914439015907 chrX 155270560 20332459 0.13094857776000807 9.618273612582872 chrY 59373566 705733 0.011886316546996688 4.550022005089289