BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013326.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 = 1,993,155 number of mapped reads = 1,461,532 (73.33%) number of supplementary alignments = 8,302 (0.42%) number of secondary alignments = 0 number of mapped bases = 88,498,304 bp number of sequenced bases = 88,459,084 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,072 duplication rate = 3.3% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0593 >>>>>>> ACTG content number of A's = 25,552,138 bp (28.89%) number of C's = 14,664,039 bp (16.58%) number of T's = 27,455,839 bp (31.04%) number of G's = 20,756,371 bp (23.46%) number of N's = 30,697 bp (0.03%) GC percentage = 40.04% >>>>>>> Mismatches and indels general error rate = 0.0109 number of mismatches = 956,336 number of insertions = 5,615 mapped reads with insertion percentage = 0.38% number of deletions = 23,769 mapped reads with deletion percentage = 1.61% homopolymer indels = 49.23% >>>>>>> Coverage mean coverageData = 0.0286X std coverageData = 0.2218X There is a 2.51% of reference with a coverageData >= 1X There is a 0.27% of reference with a coverageData >= 2X There is a 0.05% of reference with a coverageData >= 3X There is a 0.01% 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 6837027 0.02743033085562503 0.27788970885571046 chr2 243199373 10799427 0.044405653134640274 0.27071851090096627 chr3 198022430 5703579 0.028802691695077168 0.19002092221645928 chr4 191154276 5546963 0.02901825225191405 0.19446660093105167 chr5 180915260 4507753 0.02491637797718114 0.17804725352348097 chr6 171115067 4544037 0.026555446458727098 0.2090299935255622 chr7 159138663 5632675 0.03539476135978345 0.3428581728350363 chr8 146364022 5204522 0.03555875227315084 0.27471339570026604 chr9 141213431 3043250 0.021550712127375474 0.1861614560415528 chr10 135534747 4303090 0.031748980208005255 0.2161024871907519 chr11 135006516 3610625 0.026744079522798735 0.20209623852793718 chr12 133851895 4490912 0.033551351663717574 0.2068794293022041 chr13 115169878 1531594 0.013298564056827429 0.12639353199884476 chr14 107349540 3070057 0.028598697302289325 0.19200503405658131 chr15 102531392 2553334 0.024902948747638185 0.19233207893789864 chr16 90354753 2643670 0.029258781771004345 0.19558785960940836 chr17 81195210 2143167 0.026395239325078413 0.19291795940278433 chr18 78077248 1961245 0.0251192895528285 0.23477859285213287 chr19 59128983 1484960 0.025113910719553555 0.21875411731572994 chr20 63025520 1775026 0.028163607376821324 0.19225544612624124 chr21 48129895 1638105 0.03403508360032782 0.21379718375373363 chr22 51304566 658298 0.01283117763826323 0.12475710565623489 chrMT 16571 15414 0.930179228773158 1.302831114025937 chrX 155270560 4640954 0.029889465201903054 0.20288297323525284 chrY 59373566 158620 0.002671559259216467 0.05937484591150437