BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716538.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 = 436,039 number of mapped reads = 399,983 (91.73%) number of supplementary alignments = 1,593 (0.37%) number of secondary alignments = 0 number of mapped bases = 23,212,397 bp number of sequenced bases = 23,205,346 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 7,797 duplication rate = 1.54% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2374 >>>>>>> ACTG content number of A's = 5,984,953 bp (25.79%) number of C's = 4,733,505 bp (20.4%) number of T's = 7,064,352 bp (30.44%) number of G's = 5,421,843 bp (23.36%) number of N's = 693 bp (0%) GC percentage = 43.76% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 117,517 number of insertions = 1,852 mapped reads with insertion percentage = 0.46% number of deletions = 4,480 mapped reads with deletion percentage = 1.11% homopolymer indels = 41.17% >>>>>>> Coverage mean coverageData = 0.0075X std coverageData = 0.1031X There is a 0.72% of reference with a coverageData >= 1X There is a 0.02% of reference with a coverageData >= 2X There is a 0% 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 1898300 0.0076160291692914175 0.15112421352918684 chr2 243199373 1984072 0.008158211822363539 0.12116075527943948 chr3 198022430 1521440 0.00768317003280891 0.09036486164820594 chr4 191154276 1499160 0.00784267049302104 0.0933887409283639 chr5 180915260 1395423 0.007713130445712539 0.09059080823961305 chr6 171115067 1314354 0.007681112032057353 0.09519103223998168 chr7 159138663 1286978 0.008087148501429851 0.11366481166818648 chr8 146364022 1164169 0.007953928732567898 0.10212821046897179 chr9 141213431 948268 0.00671514029001958 0.09047067336239652 chr10 135534747 1114258 0.00822119806664781 0.1043637600609147 chr11 135006516 1030761 0.007634898155582357 0.09765331642249837 chr12 133851895 1058502 0.007908009072266029 0.09186526748680879 chr13 115169878 715635 0.006213734115442929 0.08118179883949707 chr14 107349540 712030 0.006632818361401455 0.08451305612448093 chr15 102531392 671796 0.006552100648355578 0.08352997098786594 chr16 90354753 678355 0.007507684736850534 0.09093183146714107 chr17 81195210 639164 0.007871942199546008 0.09214519527549468 chr18 78077248 606921 0.007773340064444894 0.12810445965311643 chr19 59128983 491470 0.008311829073738678 0.12413366057898506 chr20 63025520 497045 0.007886408553233673 0.09267994012385136 chr21 48129895 307957 0.006398455679157413 0.08399065691989642 chr22 51304566 286674 0.005587689797434404 0.07707975408515905 chrMT 16571 7590 0.4580290869591455 0.6967856987330029 chrX 155270560 1308246 0.008425589500031428 0.09736125016236484 chrY 59373566 73829 0.0012434658211366318 0.04702312380103079