BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716243.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 788,948 number of mapped reads = 746,329 (94.6%) number of supplementary alignments = 12,452 (1.58%) number of secondary alignments = 0 number of mapped bases = 60,216,102 bp number of sequenced bases = 60,189,491 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 24,092 duplication rate = 1.76% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7072 >>>>>>> ACTG content number of A's = 15,502,814 bp (25.76%) number of C's = 11,524,556 bp (19.15%) number of T's = 18,277,257 bp (30.37%) number of G's = 14,881,174 bp (24.72%) number of N's = 3,690 bp (0.01%) GC percentage = 43.87% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 476,783 number of insertions = 5,258 mapped reads with insertion percentage = 0.69% number of deletions = 15,228 mapped reads with deletion percentage = 2.01% homopolymer indels = 44.83% >>>>>>> Coverage mean coverageData = 0.0195X std coverageData = 0.2693X There is a 1.78% of reference with a coverageData >= 1X There is a 0.1% of reference with a coverageData >= 2X There is a 0.01% 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 4904361 0.019676424396952656 0.42851289799358266 chr2 243199373 5376677 0.022108103872455296 0.36654140574373023 chr3 198022430 4159769 0.02100655466150981 0.15457045757414986 chr4 191154276 3984053 0.020842081502796202 0.1608343114504069 chr5 180915260 3750061 0.020728273557465524 0.15499027268089022 chr6 171115067 3650232 0.021332031503689855 0.1794915237035994 chr7 159138663 3381678 0.02124988319149068 0.32803749245321945 chr8 146364022 3226393 0.022043620801838856 0.38030363548622687 chr9 141213431 2686936 0.01902748188307952 0.30511469748630093 chr10 135534747 2929411 0.021613726847477716 0.26665294859024785 chr11 135006516 2744093 0.020325633764225127 0.24932642981033964 chr12 133851895 2773943 0.020723972566843375 0.15600525002684443 chr13 115169878 1998714 0.017354485692864935 0.13791497342108594 chr14 107349540 1883047 0.017541267526623775 0.18525030291526695 chr15 102531392 1737497 0.016946000303984948 0.13798913839820373 chr16 90354753 1659968 0.01837167326438267 0.1694099318381596 chr17 81195210 1630788 0.020084780863304622 0.16817067832679505 chr18 78077248 1778177 0.022774586009998713 0.5869464813433175 chr19 59128983 1161301 0.01964013147325737 0.3185188891676466 chr20 63025520 1237449 0.01963409425261386 0.1570759839453894 chr21 48129895 823304 0.01710587567249004 0.14603668950987764 chr22 51304566 635441 0.012385661736228312 0.1171206907337876 chrMT 16571 11018 0.6648965059441192 0.8781436829776941 chrX 155270560 1954309 0.01258647486039852 0.1686870547318014 chrY 59373566 137482 0.002315542239790684 0.08216768510050261