BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6240075.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 = 1,593,823 number of mapped reads = 1,204,205 (75.55%) number of supplementary alignments = 8,218 (0.52%) number of secondary alignments = 0 number of mapped bases = 76,568,769 bp number of sequenced bases = 76,538,875 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 146,405 duplication rate = 9.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.8719 >>>>>>> ACTG content number of A's = 20,851,857 bp (27.24%) number of C's = 13,720,953 bp (17.93%) number of T's = 24,484,807 bp (31.99%) number of G's = 17,430,306 bp (22.77%) number of N's = 50,952 bp (0.07%) GC percentage = 40.7% >>>>>>> Mismatches and indels general error rate = 0.0086 number of mismatches = 648,389 number of insertions = 5,366 mapped reads with insertion percentage = 0.44% number of deletions = 17,505 mapped reads with deletion percentage = 1.44% homopolymer indels = 48.08% >>>>>>> Coverage mean coverageData = 0.0247X std coverageData = 0.2829X There is a 1.51% of reference with a coverageData >= 1X There is a 0.54% of reference with a coverageData >= 2X There is a 0.22% of reference with a coverageData >= 3X There is a 0.09% of reference with a coverageData >= 4X There is a 0.04% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 5723668 0.022963505475077632 0.3326691944716777 chr2 243199373 6696299 0.027534195164228486 0.329090839821294 chr3 198022430 4808878 0.024284511608104194 0.23823942792637628 chr4 191154276 5097111 0.02666490704084485 0.25684894591596497 chr5 180915260 4819598 0.02664008552954571 0.25023136925188244 chr6 171115067 5273550 0.03081873555880383 0.28631846125704014 chr7 159138663 4379411 0.027519465838417908 0.2920636385619451 chr8 146364022 3707633 0.02533158729404143 0.44714544890693675 chr9 141213431 4019429 0.02846350358840867 0.28716874579875984 chr10 135534747 3575161 0.026378187727756634 0.2753074270348854 chr11 135006516 3057327 0.02264577363065943 0.25226358158231 chr12 133851895 3418412 0.025538764318577635 0.2493173938100109 chr13 115169878 2508442 0.021780365174998276 0.22717591076213978 chr14 107349540 2331797 0.021721536953022806 0.23344766367582792 chr15 102531392 2084528 0.020330632007804984 0.2271503346782636 chr16 90354753 2140417 0.02368903603776107 0.24014608156012615 chr17 81195210 2183501 0.02689199276656837 0.2543258449789645 chr18 78077248 2375044 0.030419156166979655 0.41378177213548006 chr19 59128983 1282315 0.02168674201617843 0.28151191247436413 chr20 63025520 1279429 0.020300173643946134 0.21885822258039522 chr21 48129895 1002294 0.02082477013506886 0.22358329366199284 chr22 51304566 759028 0.014794550644868528 0.18239459218359297 chrMT 16571 14158 0.8543841651077183 1.442303126013476 chrX 155270560 3838941 0.02472420399591526 0.24958001644369884 chrY 59373566 192398 0.003240465630782561 0.08448478750188684