BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231856.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 = 1,409,648 number of mapped reads = 954,647 (67.72%) number of supplementary alignments = 4,639 (0.33%) number of secondary alignments = 0 number of mapped bases = 62,164,509 bp number of sequenced bases = 62,130,550 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 31,420 duplication rate = 2.65% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.3184 >>>>>>> ACTG content number of A's = 17,044,776 bp (27.43%) number of C's = 11,301,567 bp (18.19%) number of T's = 19,678,768 bp (31.67%) number of G's = 14,102,350 bp (22.7%) number of N's = 3,089 bp (0%) GC percentage = 40.89% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 478,287 number of insertions = 4,779 mapped reads with insertion percentage = 0.49% number of deletions = 19,263 mapped reads with deletion percentage = 2% homopolymer indels = 45% >>>>>>> Coverage mean coverageData = 0.0201X std coverageData = 0.2149X There is a 1.82% of reference with a coverageData >= 1X There is a 0.14% of reference with a coverageData >= 2X There is a 0.02% of reference with a coverageData >= 3X There is a 0% 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 6253298 0.02508839486502222 0.42138687973886707 chr2 243199373 5149042 0.021172102281694617 0.2579653108151545 chr3 198022430 5038241 0.025442779386153375 0.17169382383439086 chr4 191154276 3044789 0.015928437823697964 0.14202220731438578 chr5 180915260 3824638 0.02114049417390219 0.15686233896856738 chr6 171115067 3841704 0.022450997842288194 0.18452626010038436 chr7 159138663 2354074 0.014792596315830553 0.18173410391606082 chr8 146364022 3475900 0.023748322521500536 0.24417449824744816 chr9 141213431 2684097 0.019007377563115792 0.1801562390948848 chr10 135534747 3009925 0.022207773774794444 0.21035920283829165 chr11 135006516 2320306 0.017186622310881645 0.16556424823622184 chr12 133851895 2415833 0.018048552842677347 0.14534102126423243 chr13 115169878 2699997 0.023443603890941 0.16473258886008688 chr14 107349540 1940972 0.01808085996456063 0.14970820470580745 chr15 102531392 1284414 0.01252703172117277 0.12116029648156289 chr16 90354753 1820502 0.02014838112611519 0.16500105014050911 chr17 81195210 1873036 0.023068306615624246 0.16865498386658198 chr18 78077248 1490794 0.01909383384004518 0.29969149773407433 chr19 59128983 1633268 0.027622122301680718 0.28950553622637776 chr20 63025520 1481634 0.023508477200981443 0.16816554926710006 chr21 48129895 995559 0.020684836316389222 0.16129910544226195 chr22 51304566 548322 0.010687586753974295 0.11100583366359945 chrMT 16571 13783 0.83175426950697 1.0296308706710315 chrX 155270560 2826963 0.018206690308838973 0.1545930307332433 chrY 59373566 143418 0.002415519391238855 0.06850807476645586