BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716805.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 = 1,003,853 number of mapped reads = 898,100 (89.47%) number of supplementary alignments = 4,034 (0.4%) number of secondary alignments = 0 number of mapped bases = 51,812,896 bp number of sequenced bases = 51,797,605 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 23,890 duplication rate = 2.04% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7373 >>>>>>> ACTG content number of A's = 12,883,461 bp (24.87%) number of C's = 10,010,080 bp (19.33%) number of T's = 16,279,773 bp (31.43%) number of G's = 12,623,587 bp (24.37%) number of N's = 704 bp (0%) GC percentage = 43.7% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 261,505 number of insertions = 3,603 mapped reads with insertion percentage = 0.4% number of deletions = 9,694 mapped reads with deletion percentage = 1.07% homopolymer indels = 41.73% >>>>>>> Coverage mean coverageData = 0.0167X std coverageData = 0.173X There is a 1.55% of reference with a coverageData >= 1X There is a 0.09% 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 4203546 0.016864736316945825 0.2840526595240546 chr2 243199373 4341865 0.017853109349915963 0.21179211519899635 chr3 198022430 3438896 0.017366194324552022 0.14012376693454662 chr4 191154276 3260860 0.017058786589738646 0.14503481020496808 chr5 180915260 3081498 0.017032825202252147 0.13868447196421765 chr6 171115067 2978545 0.017406678746764014 0.15191095275123254 chr7 159138663 2874759 0.018064491342371022 0.20152358372040455 chr8 146364022 2607860 0.017817630073051694 0.1621038280510279 chr9 141213431 2175921 0.015408739697005167 0.15268389023922135 chr10 135534747 2482758 0.018318239823770063 0.17090973433983322 chr11 135006516 2389466 0.0176988938815368 0.1606381553287578 chr12 133851895 2348965 0.017548985765199664 0.14164039027047493 chr13 115169878 1585057 0.013762773978105628 0.12463301975964668 chr14 107349540 1522295 0.014180731468434796 0.1311874581898011 chr15 102531392 1499299 0.014622828879568903 0.12915165944871088 chr16 90354753 1527224 0.016902530849705274 0.14373857409541013 chr17 81195210 1471955 0.018128594038983335 0.14840727306031717 chr18 78077248 1347628 0.01726018826893079 0.21808741333112217 chr19 59128983 1133838 0.01917567227564188 0.21939540293812002 chr20 63025520 1123792 0.017830745386948017 0.14247572907847864 chr21 48129895 668473 0.013888935348809715 0.13348206334533752 chr22 51304566 651936 0.012707173080852101 0.11916288295971847 chrMT 16571 4938 0.29799046527065354 0.5499887854691081 chrX 155270560 2926141 0.01884543341635401 0.15516408243213894 chrY 59373566 165381 0.0027854314830946824 0.08187996546632073