BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3472419.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP074289/SRP074289.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 = 20,758,788 number of mapped reads = 20,572,785 (99.1%) number of supplementary alignments = 88,282 (0.43%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 10,331,311 number of mapped paired reads (second in pair) = 10,241,474 number of mapped paired reads (both in pair) = 20,439,666 number of mapped paired reads (singletons) = 133,119 number of mapped bases = 2,023,111,084 bp number of sequenced bases = 2,022,823,610 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 12,989,853 duplication rate = 46.95% >>>>>>> Insert size mean insert size = 22,912.2325 std insert size = 1,442,252.9705 median insert size = 240 >>>>>>> Mapping quality mean mapping quality = 54.9705 >>>>>>> ACTG content number of A's = 556,920,452 bp (27.53%) number of C's = 455,938,102 bp (22.54%) number of T's = 558,447,002 bp (27.61%) number of G's = 451,270,520 bp (22.31%) number of N's = 247,534 bp (0.01%) GC percentage = 44.85% >>>>>>> Mismatches and indels general error rate = 0.006 number of mismatches = 11,962,575 number of insertions = 123,921 mapped reads with insertion percentage = 0.6% number of deletions = 113,050 mapped reads with deletion percentage = 0.54% homopolymer indels = 47.22% >>>>>>> Coverage mean coverageData = 0.6535X std coverageData = 19.6837X There is a 6.03% of reference with a coverageData >= 1X There is a 2.51% of reference with a coverageData >= 2X There is a 1.07% of reference with a coverageData >= 3X There is a 0.76% of reference with a coverageData >= 4X There is a 0.57% of reference with a coverageData >= 5X There is a 0.51% of reference with a coverageData >= 6X There is a 0.47% of reference with a coverageData >= 7X There is a 0.45% of reference with a coverageData >= 8X There is a 0.42% of reference with a coverageData >= 9X There is a 0.41% of reference with a coverageData >= 10X There is a 0.4% of reference with a coverageData >= 11X There is a 0.38% of reference with a coverageData >= 12X There is a 0.37% of reference with a coverageData >= 13X There is a 0.36% of reference with a coverageData >= 14X There is a 0.35% of reference with a coverageData >= 15X There is a 0.34% of reference with a coverageData >= 16X There is a 0.34% of reference with a coverageData >= 17X There is a 0.33% of reference with a coverageData >= 18X There is a 0.32% of reference with a coverageData >= 19X There is a 0.31% of reference with a coverageData >= 20X There is a 0.31% of reference with a coverageData >= 21X There is a 0.3% of reference with a coverageData >= 22X There is a 0.3% of reference with a coverageData >= 23X There is a 0.29% of reference with a coverageData >= 24X There is a 0.29% of reference with a coverageData >= 25X There is a 0.28% of reference with a coverageData >= 26X There is a 0.28% of reference with a coverageData >= 27X There is a 0.27% of reference with a coverageData >= 28X There is a 0.27% of reference with a coverageData >= 29X There is a 0.26% of reference with a coverageData >= 30X There is a 0.26% of reference with a coverageData >= 31X There is a 0.25% of reference with a coverageData >= 32X There is a 0.25% of reference with a coverageData >= 33X There is a 0.25% of reference with a coverageData >= 34X There is a 0.24% of reference with a coverageData >= 35X There is a 0.24% of reference with a coverageData >= 36X There is a 0.24% of reference with a coverageData >= 37X There is a 0.23% of reference with a coverageData >= 38X There is a 0.23% of reference with a coverageData >= 39X There is a 0.23% of reference with a coverageData >= 40X There is a 0.23% of reference with a coverageData >= 41X There is a 0.22% of reference with a coverageData >= 42X There is a 0.22% of reference with a coverageData >= 43X There is a 0.22% of reference with a coverageData >= 44X There is a 0.21% of reference with a coverageData >= 45X There is a 0.21% of reference with a coverageData >= 46X There is a 0.21% of reference with a coverageData >= 47X There is a 0.21% of reference with a coverageData >= 48X There is a 0.2% of reference with a coverageData >= 49X There is a 0.2% of reference with a coverageData >= 50X There is a 0.2% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 261065877 1.0474031155974532 26.55088012025973 chr2 243199373 120608953 0.495926249776968 15.621825604111509 chr3 198022430 150531664 0.7601748145399488 20.11912946010419 chr4 191154276 67988275 0.3556722686130233 10.29938153617609 chr5 180915260 150910518 0.8341502977692429 27.424945224943077 chr6 171115067 143532541 0.8388071460708951 19.689141648182744 chr7 159138663 117970232 0.7413046570587313 20.641956734983196 chr8 146364022 104938191 0.7169671177798052 18.38773673874918 chr9 141213431 58149189 0.41178228294729274 12.128453021923374 chr10 135534747 53476895 0.39456225199579265 10.79530589562815 chr11 135006516 92602084 0.6859082564577846 17.937762905497465 chr12 133851895 100464798 0.7505668709434409 20.95181955184605 chr13 115169878 48369631 0.419985084988976 17.952006327281698 chr14 107349540 60797186 0.5663478949234435 15.962646848015062 chr15 102531392 47533003 0.46359463255897276 12.941789138150048 chr16 90354753 131106005 1.4510139272916833 43.42421135750485 chr17 81195210 53797733 0.6625727428994888 19.546404693793836 chr18 78077248 36280489 0.4646742800156071 13.50952148632157 chr19 59128983 56363750 0.9532338819356998 24.16199008565493 chr20 63025520 38428215 0.6097246797805079 14.574877908367817 chr21 48129895 16058754 0.33365445738038696 16.472961793870663 chr22 51304566 26686444 0.5201572897040002 13.396812797024243 chrMT 16571 8971 0.5413674491581679 0.9325315800359211 chrX 155270560 85013588 0.5475190403126001 15.597533500120424 chrY 59373566 428098 0.007210245717766051 0.4832696797206398