BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549124.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 15,446,038 number of mapped reads = 9,112,334 (58.99%) number of secondary alignments = 0 number of mapped bases = 359,160,770 bp number of sequenced bases = 359,118,060 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 793,659 duplication rate = 7.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.5499 >>>>>>> ACTG content number of A's = 98,355,870 bp (27.39%) number of C's = 80,537,672 bp (22.43%) number of T's = 99,424,307 bp (27.69%) number of G's = 80,785,750 bp (22.5%) number of N's = 14,461 bp (0%) GC percentage = 44.92% >>>>>>> Mismatches and indels general error rate = 0.0038 number of mismatches = 1,343,076 number of insertions = 13,238 mapped reads with insertion percentage = 0.15% number of deletions = 34,319 mapped reads with deletion percentage = 0.38% homopolymer indels = 43.06% >>>>>>> Coverage mean coverageData = 0.116X std coverageData = 0.8414X There is a 7.11% of reference with a coverageData >= 1X There is a 2.27% of reference with a coverageData >= 2X There is a 0.99% of reference with a coverageData >= 3X There is a 0.49% of reference with a coverageData >= 4X There is a 0.26% of reference with a coverageData >= 5X There is a 0.14% of reference with a coverageData >= 6X There is a 0.08% 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 0.02% 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 30197126 0.12115165803338158 1.1764774203352668 chr2 243199373 29356956 0.12071147897243963 0.7078631971734296 chr3 198022430 22419148 0.11321519486454136 0.5262654724284618 chr4 191154276 20674162 0.10815432661312792 0.5785538349748331 chr5 180915260 20389342 0.11270106236477785 0.5412256354788213 chr6 171115067 19240517 0.11244198034297004 0.5396826102669716 chr7 159138663 20217074 0.12704061740169326 0.8244401561072178 chr8 146364022 17517116 0.1196818436705709 2.0910073282517128 chr9 141213431 15787442 0.11179844500768486 0.6658823330538983 chr10 135534747 17723593 0.13076789083466545 0.751468777084755 chr11 135006516 16811606 0.124524404436894 0.6251338612677193 chr12 133851895 16323138 0.12194924845852947 0.5672116970100038 chr13 115169878 10029539 0.08708474102924725 0.4614924199066403 chr14 107349540 11138824 0.10376219590694101 0.8147623261015337 chr15 102531392 11390518 0.11109298116229613 0.5189672386601165 chr16 90354753 13129144 0.14530662266322614 0.6480479970885608 chr17 81195210 13156070 0.16203012468346348 0.6504692529003783 chr18 78077248 8792129 0.11260808014134925 1.183932247824742 chr19 59128983 10842610 0.18337217130895014 1.2877858940825262 chr20 63025520 8851862 0.14044885309950636 0.63331994786213 chr21 48129895 4977480 0.10341763679309918 0.6050025791935986 chr22 51304566 6379171 0.1243392449709057 0.5796110275545783 chrMT 16571 181415 10.94774002775934 13.978041582695012 chrX 155270560 10739518 0.0691664794665518 0.46849459417103567 chrY 59373566 2895270 0.048763619823677086 0.5153102774015809