BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1708530.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP051114/SRP051114.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 = 3,202,887 number of mapped reads = 2,194,173 (68.51%) number of supplementary alignments = 1,289 (0.04%) number of secondary alignments = 0 number of mapped bases = 103,883,644 bp number of sequenced bases = 103,863,197 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 85,224 duplication rate = 2.67% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 41.4525 >>>>>>> ACTG content number of A's = 29,735,809 bp (28.63%) number of C's = 19,054,106 bp (18.35%) number of T's = 33,332,835 bp (32.09%) number of G's = 21,739,012 bp (20.93%) number of N's = 1,435 bp (0%) GC percentage = 39.28% >>>>>>> Mismatches and indels general error rate = 0.0053 number of mismatches = 537,935 number of insertions = 5,872 mapped reads with insertion percentage = 0.27% number of deletions = 13,400 mapped reads with deletion percentage = 0.61% homopolymer indels = 46.31% >>>>>>> Coverage mean coverageData = 0.0336X std coverageData = 0.4011X There is a 3.06% of reference with a coverageData >= 1X There is a 0.19% of reference with a coverageData >= 2X There is a 0.02% 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 8436127 0.03384596181206706 0.7992152110899818 chr2 243199373 9157470 0.037654167800835574 0.3259871945115553 chr3 198022430 7307283 0.03690128941453753 0.20859617867235458 chr4 191154276 6938233 0.03629650952720514 0.2124589878527941 chr5 180915260 6650300 0.036759198754157056 0.2095421436566833 chr6 171115067 6316544 0.036914014123607244 0.2580961227574695 chr7 159138663 5976398 0.0375546576007114 0.5060276047619132 chr8 146364022 5499429 0.03757363951094484 0.9114745833459174 chr9 141213431 4348072 0.030790782216742543 0.25041035810425305 chr10 135534747 4897369 0.03613367869421706 0.28353781845775144 chr11 135006516 4789360 0.035475028479366136 0.37353844827579097 chr12 133851895 4806787 0.035911236071779186 0.2104173846184361 chr13 115169878 3489778 0.030301134815823978 0.1885083445575659 chr14 107349540 3289332 0.030641323661004975 0.19969860364355888 chr15 102531392 2979821 0.029062523602527507 0.18339831724521216 chr16 90354753 2757142 0.030514631587781553 0.19817162306577765 chr17 81195210 2659348 0.03275252320918931 0.28824826295064615 chr18 78077248 2824709 0.03617838835713062 0.43143273086714956 chr19 59128983 1869504 0.031617388041326536 0.5189116055345623 chr20 63025520 2085596 0.03309129381241123 0.196638661868191 chr21 48129895 1394372 0.02897101687007628 0.22993732022620444 chr22 51304566 1095423 0.02135137445661269 0.17949894501952127 chrMT 16571 169610 10.235350914247782 7.855425375098554 chrX 155270560 3425556 0.02206185126143681 0.20361341398167476 chrY 59373566 720081 0.0121279729096952 0.13688795655017086