BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004107.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 = 2,942,124 number of mapped reads = 2,144,858 (72.9%) number of supplementary alignments = 11,405 (0.39%) number of secondary alignments = 0 number of mapped bases = 136,777,990 bp number of sequenced bases = 136,696,700 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 139,797 duplication rate = 5.33% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.5418 >>>>>>> ACTG content number of A's = 35,351,462 bp (25.86%) number of C's = 24,396,353 bp (17.85%) number of T's = 44,807,547 bp (32.78%) number of G's = 32,124,298 bp (23.5%) number of N's = 17,040 bp (0.01%) GC percentage = 41.35% >>>>>>> Mismatches and indels general error rate = 0.0108 number of mismatches = 1,463,623 number of insertions = 11,800 mapped reads with insertion percentage = 0.54% number of deletions = 49,668 mapped reads with deletion percentage = 2.28% homopolymer indels = 47.83% >>>>>>> Coverage mean coverageData = 0.0442X std coverageData = 0.4024X There is a 3.4% of reference with a coverageData >= 1X There is a 0.7% of reference with a coverageData >= 2X There is a 0.17% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 11891742 0.047709979426691175 0.6464752564641418 chr2 243199373 11280425 0.046383446062585036 0.5384776450458111 chr3 198022430 8615577 0.04350808643243091 0.26052848736259443 chr4 191154276 9165587 0.04794863704749142 0.2841102167100043 chr5 180915260 7831801 0.04328988610468791 0.26079441410393833 chr6 171115067 8108171 0.04738431946498317 0.30930191665845436 chr7 159138663 8459022 0.053155040016893945 0.6563145151496307 chr8 146364022 8647693 0.05908346109811057 0.44647848968138065 chr9 141213431 4932761 0.03493124531476046 0.3714674286651724 chr10 135534747 6530526 0.048183407904985424 0.33349958594971163 chr11 135006516 5853470 0.0433569443418568 0.36918063984868704 chr12 133851895 5978359 0.044663984772124445 0.2682863820007489 chr13 115169878 3925933 0.03408819274775997 0.23032696477772327 chr14 107349540 3360237 0.03130182951878508 0.24969030203202314 chr15 102531392 3589435 0.035008156331282424 0.2416170715148854 chr16 90354753 4052958 0.04485605754464295 0.28497633143988266 chr17 81195210 3377261 0.04159433789259243 0.27687087410296984 chr18 78077248 3960366 0.05072368841688683 0.679412210343714 chr19 59128983 2449075 0.041419197079713005 0.430235585416638 chr20 63025520 3273582 0.051940578990859576 0.3015825591466406 chr21 48129895 2033042 0.04224073208553644 0.27341952130674296 chr22 51304566 1539324 0.030003645289583 0.21389687050808076 chrMT 16571 123361 7.444390803210428 5.617432893559586 chrX 155270560 7441218 0.047924204047438225 0.3118844979810383 chrY 59373566 357064 0.006013854717771204 0.12240052900850065