BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013268.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP116771/SRP116771.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 = 2,051,592 number of mapped reads = 1,833,014 (89.35%) number of supplementary alignments = 8,809 (0.43%) number of secondary alignments = 0 number of mapped bases = 122,844,661 bp number of sequenced bases = 122,791,874 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 74,242 duplication rate = 3.03% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.4899 >>>>>>> ACTG content number of A's = 34,322,262 bp (27.95%) number of C's = 22,292,227 bp (18.15%) number of T's = 39,225,546 bp (31.94%) number of G's = 26,924,806 bp (21.93%) number of N's = 27,033 bp (0.02%) GC percentage = 40.08% >>>>>>> Mismatches and indels general error rate = 0.0082 number of mismatches = 984,018 number of insertions = 9,274 mapped reads with insertion percentage = 0.5% number of deletions = 30,880 mapped reads with deletion percentage = 1.67% homopolymer indels = 45.72% >>>>>>> Coverage mean coverageData = 0.0397X std coverageData = 0.3981X There is a 3.45% of reference with a coverageData >= 1X There is a 0.37% of reference with a coverageData >= 2X There is a 0.05% 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% 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 9432038 0.03784158274975772 0.6314778637612362 chr2 243199373 15842964 0.06514393439657429 0.5009736256035501 chr3 198022430 9846617 0.0497247559279017 0.24710953824227314 chr4 191154276 9367621 0.04900555298067201 0.2554677280623115 chr5 180915260 6197917 0.03425867447555281 0.2055526104962135 chr6 171115067 7414696 0.04333163718423463 0.2965875036233773 chr7 159138663 7352579 0.046202342418825024 0.8814818592842185 chr8 146364022 7002133 0.047840534199039705 0.44636129890691456 chr9 141213431 4699926 0.033282429062997554 0.32797984605597397 chr10 135534747 4394514 0.03242352309847157 0.3994534463232381 chr11 135006516 4563739 0.03380384247527727 0.2475027763652883 chr12 133851895 6103809 0.045601214685828693 0.2442718096196153 chr13 115169878 2625563 0.022797306427640742 0.16829401058672963 chr14 107349540 3608498 0.03361447100751433 0.22897213065020647 chr15 102531392 2283258 0.022268867665426798 0.16783896371236437 chr16 90354753 2432885 0.026925921650187014 0.2068332886802472 chr17 81195210 3170935 0.03905322740097599 0.22732268284531537 chr18 78077248 3261209 0.04176900548543924 0.5895391907704378 chr19 59128983 1816163 0.030715275451296025 0.4712077367886525 chr20 63025520 2084912 0.0330804410657778 0.20600586110851934 chr21 48129895 1875000 0.03895707646983231 0.23173883794128994 chr22 51304566 1265791 0.02467209253850817 0.17302065978674322 chrMT 16571 71806 4.3332327560195525 3.3162324938146317 chrX 155270560 5904475 0.03802700911235201 0.23630597832188907 chrY 59373566 225613 0.0037998896680721517 0.09942514551020076