BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549143.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 = 13,420,015 number of mapped reads = 11,782,554 (87.8%) number of secondary alignments = 0 number of mapped bases = 467,405,803 bp number of sequenced bases = 467,358,328 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 641,594 duplication rate = 4.29% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.6063 >>>>>>> ACTG content number of A's = 132,158,892 bp (28.28%) number of C's = 100,302,173 bp (21.46%) number of T's = 134,158,439 bp (28.71%) number of G's = 100,645,126 bp (21.53%) number of N's = 93,698 bp (0.02%) GC percentage = 43% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 1,469,825 number of insertions = 12,369 mapped reads with insertion percentage = 0.1% number of deletions = 37,482 mapped reads with deletion percentage = 0.32% homopolymer indels = 45.83% >>>>>>> Coverage mean coverageData = 0.151X std coverageData = 0.8722X There is a 10.64% of reference with a coverageData >= 1X There is a 2.89% of reference with a coverageData >= 2X There is a 0.88% of reference with a coverageData >= 3X There is a 0.29% of reference with a coverageData >= 4X There is a 0.11% of reference with a coverageData >= 5X There is a 0.05% of reference with a coverageData >= 6X There is a 0.02% 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% 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 38583540 0.1547981699913197 1.6020190810638877 chr2 243199373 39579372 0.16274454786526116 0.8582216473211011 chr3 198022430 31142151 0.1572657753972618 0.5294276103503007 chr4 191154276 28810827 0.15072028522134656 0.5454572631051205 chr5 180915260 28581544 0.15798304686956754 0.543576109690572 chr6 171115067 26644922 0.15571347670979785 0.6051840446324106 chr7 159138663 26598373 0.16713960327792876 1.3480150167417577 chr8 146364022 23769550 0.16240022428462644 0.7753471550058482 chr9 141213431 19930003 0.14113390531528122 0.810539728808422 chr10 135534747 22882871 0.16883398173901487 0.8039520961312379 chr11 135006516 21829983 0.16169577326178836 0.7547126466800054 chr12 133851895 21420307 0.16002991216523307 0.5699139090479862 chr13 115169878 14253531 0.12376092818297507 0.4578657554677959 chr14 107349540 14653006 0.13649807907886705 0.7243323306357705 chr15 102531392 14407107 0.14051410713315976 0.4974136529034288 chr16 90354753 14902308 0.16493109111813964 0.6113833402578083 chr17 81195210 14199524 0.17488130149549463 0.625363058274607 chr18 78077248 12241076 0.15678160172858552 1.688408720169394 chr19 59128983 11214502 0.18966167573015758 1.4531363549381189 chr20 63025520 10846016 0.17208927431300844 0.5938509733900984 chr21 48129895 6201262 0.12884428690318148 0.5879785639120872 chr22 51304566 6505153 0.12679481588441854 0.5214621184936302 chrMT 16571 7631 0.46050328887816067 0.8166283524746499 chrX 155270560 14720066 0.09480268506792273 0.5412598597244398 chrY 59373566 3481178 0.05863178236591011 0.43136210712846845