BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1549134.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 = 12,459,767 number of mapped reads = 10,816,319 (86.81%) number of secondary alignments = 0 number of mapped bases = 429,481,704 bp number of sequenced bases = 429,440,312 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 581,242 duplication rate = 4.25% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.0363 >>>>>>> ACTG content number of A's = 125,859,017 bp (29.31%) number of C's = 88,551,365 bp (20.62%) number of T's = 126,836,031 bp (29.54%) number of G's = 88,099,543 bp (20.51%) number of N's = 94,356 bp (0.02%) GC percentage = 41.14% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 1,374,203 number of insertions = 10,760 mapped reads with insertion percentage = 0.1% number of deletions = 32,714 mapped reads with deletion percentage = 0.3% homopolymer indels = 45.39% >>>>>>> Coverage mean coverageData = 0.1387X std coverageData = 1.089X There is a 9.7% of reference with a coverageData >= 1X There is a 2.76% of reference with a coverageData >= 2X There is a 0.82% of reference with a coverageData >= 3X There is a 0.26% of reference with a coverageData >= 4X There is a 0.09% of reference with a coverageData >= 5X There is a 0.04% 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% 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 36054483 0.1446515272674085 1.6220876081323026 chr2 243199373 36780013 0.15123399598567222 0.7251266714286371 chr3 198022430 29616516 0.1495614208956026 0.5140609053241676 chr4 191154276 28885892 0.1511129785032902 0.5577885056599249 chr5 180915260 26629678 0.14719420572924583 0.5228289816086991 chr6 171115067 25354867 0.14817436853763438 0.5590077910946082 chr7 159138663 23747035 0.14922228547314112 1.1233955124975676 chr8 146364022 22213916 0.15177169700898216 3.4668589368920353 chr9 141213431 17914871 0.1268637896065283 0.6676286401184148 chr10 135534747 20430381 0.15073906472116705 0.7491476568232727 chr11 135006516 20048916 0.14850332112858908 0.6705594302258705 chr12 133851895 19806765 0.147975230384299 0.5318116228801615 chr13 115169878 14119335 0.12259572767803054 0.4624797166236943 chr14 107349540 13486426 0.12563096218204567 0.593111247530891 chr15 102531392 13143517 0.12819017418587275 0.469428706263597 chr16 90354753 12096974 0.1338830952257708 0.5298284409712148 chr17 81195210 11819579 0.14556990492419442 0.5523444620632755 chr18 78077248 11594476 0.14850005983817463 1.3174860084163844 chr19 59128983 8122583 0.13737058525089127 1.3064854937607104 chr20 63025520 9100591 0.14439533382667846 0.5391470791479318 chr21 48129895 5505496 0.11438828196072316 0.5295061790437012 chr22 51304566 5014850 0.09774666059937043 0.4404663093999608 chrMT 16571 166939 10.074165711182186 12.174582219264906 chrX 155270560 14316085 0.09220089758161495 0.49683824734003007 chrY 59373566 3511520 0.05914281786611907 0.5549975659920314