BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3085051.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,867,505 number of mapped reads = 1,693,197 (90.67%) number of supplementary alignments = 14,534 (0.78%) number of secondary alignments = 0 number of mapped bases = 112,163,992 bp number of sequenced bases = 112,124,038 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 52,918 duplication rate = 2.39% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8929 >>>>>>> ACTG content number of A's = 32,661,180 bp (29.13%) number of C's = 21,131,913 bp (18.85%) number of T's = 34,805,133 bp (31.04%) number of G's = 23,513,145 bp (20.97%) number of N's = 12,667 bp (0.01%) GC percentage = 39.82% >>>>>>> Mismatches and indels general error rate = 0.0091 number of mismatches = 1,001,648 number of insertions = 7,886 mapped reads with insertion percentage = 0.46% number of deletions = 23,328 mapped reads with deletion percentage = 1.36% homopolymer indels = 45.92% >>>>>>> Coverage mean coverageData = 0.0362X std coverageData = 0.3296X There is a 3.19% of reference with a coverageData >= 1X There is a 0.32% of reference with a coverageData >= 2X There is a 0.04% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0% 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 9154297 0.03672727860525571 0.4762577605482411 chr2 243199373 11476411 0.0471893116270493 0.3638284227656562 chr3 198022430 7044711 0.035575318412161695 0.2175015187810141 chr4 191154276 7486064 0.03916241978285644 0.22179155586836205 chr5 180915260 5730716 0.03167624444726221 0.19515051770608813 chr6 171115067 7666412 0.04480267070812648 0.2992556923837258 chr7 159138663 10233434 0.0643051399772034 0.38082454670763943 chr8 146364022 6346776 0.04336295158655862 0.7218625800424541 chr9 141213431 3434040 0.024318083454823784 0.2648594806066334 chr10 135534747 7734450 0.05706617801854162 0.4660298497437866 chr11 135006516 4475258 0.03314845929362402 0.2443503544571167 chr12 133851895 4897828 0.03659139827643083 0.2143622184844932 chr13 115169878 2554565 0.022180843154144873 0.16218841974703876 chr14 107349540 3849771 0.035862016735237055 0.2243603116495378 chr15 102531392 2087425 0.020358886769039478 0.15830169172317296 chr16 90354753 2663323 0.029476291081222922 0.2045990091228801 chr17 81195210 1719948 0.021182875196701874 0.1811986868405693 chr18 78077248 2496598 0.03197599894914329 0.4380628146139887 chr19 59128983 1500172 0.025371178800758336 0.35445785632607124 chr20 63025520 2552488 0.040499277118221315 0.22301675540343155 chr21 48129895 1255810 0.026092099307509397 0.18401119904666127 chr22 51304566 633849 0.012354631359711727 0.1202244099024002 chrMT 16571 15551 0.9384466839659646 1.1310999395577637 chrX 155270560 4924389 0.031714891734788614 0.2182792565218897 chrY 59373566 229706 0.003868826069837207 0.08651788581603759