BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1818860.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP055057/SRP055057.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 = 747,751 number of mapped reads = 683,054 (91.35%) number of supplementary alignments = 12,606 (1.69%) number of secondary alignments = 0 number of mapped bases = 63,137,008 bp number of sequenced bases = 63,095,060 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 116,286 duplication rate = 14.47% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.0877 >>>>>>> ACTG content number of A's = 18,110,864 bp (28.7%) number of C's = 12,747,890 bp (20.2%) number of T's = 18,399,333 bp (29.16%) number of G's = 13,835,990 bp (21.93%) number of N's = 983 bp (0%) GC percentage = 42.13% >>>>>>> Mismatches and indels general error rate = 0.0065 number of mismatches = 390,251 number of insertions = 8,944 mapped reads with insertion percentage = 1.27% number of deletions = 21,534 mapped reads with deletion percentage = 3.07% homopolymer indels = 41.38% >>>>>>> Coverage mean coverageData = 0.0204X std coverageData = 0.2714X There is a 1.58% of reference with a coverageData >= 1X There is a 0.3% of reference with a coverageData >= 2X There is a 0.07% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% 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 5673608 0.02276266344788766 0.3940895417375975 chr2 243199373 4587478 0.01886303382862751 0.38757829236786057 chr3 198022430 3681976 0.01859373203328532 0.1703981366603221 chr4 191154276 3698429 0.01934787480244491 0.19034563260531162 chr5 180915260 3323721 0.018371700651454166 0.17165565467832317 chr6 171115067 2989655 0.017471605817154606 0.17274686586181323 chr7 159138663 5416567 0.03403677583994783 0.48270074664314855 chr8 146364022 6074031 0.041499481341118104 0.2892482587661294 chr9 141213431 2247802 0.015917763516417924 0.2267198820767482 chr10 135534747 2783584 0.020537788733984208 0.33463752288985493 chr11 135006516 2612554 0.019351317828244674 0.1923809369702274 chr12 133851895 2334151 0.017438311202093926 0.1633671083063299 chr13 115169878 1556509 0.013514896664212843 0.14301827529184685 chr14 107349540 2056154 0.01915382217753332 0.17957215782367328 chr15 102531392 1652375 0.016115796028595808 0.15355926945198395 chr16 90354753 1527971 0.01691079826204605 0.28817296510760143 chr17 81195210 1622383 0.019981264904666174 0.20022316514811808 chr18 78077248 1094318 0.014015837238525621 0.2593170203802094 chr19 59128983 1140281 0.019284637450977297 0.34146242018457446 chr20 63025520 2455053 0.038953316053560526 0.2544856071640875 chr21 48129895 761052 0.015812459179476705 0.16863256412826083 chr22 51304566 706923 0.013778949031554034 0.15781602219907 chrMT 16571 63937 3.85836702673345 3.425526057470363 chrX 155270560 2853318 0.01837642628454486 0.18828617731323344 chrY 59373566 223178 0.0037588781512634764 0.30218218966678667