BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10524390.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 = 4,236,983 number of mapped reads = 3,873,536 (91.42%) number of supplementary alignments = 14,323 (0.34%) number of secondary alignments = 0 number of mapped bases = 226,001,502 bp number of sequenced bases = 225,936,681 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 273,909 duplication rate = 5.24% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.7071 >>>>>>> ACTG content number of A's = 56,045,791 bp (24.81%) number of C's = 45,647,898 bp (20.2%) number of T's = 72,764,793 bp (32.21%) number of G's = 51,449,951 bp (22.77%) number of N's = 28,248 bp (0.01%) GC percentage = 42.98% >>>>>>> Mismatches and indels general error rate = 0.0051 number of mismatches = 1,106,933 number of insertions = 19,085 mapped reads with insertion percentage = 0.49% number of deletions = 41,241 mapped reads with deletion percentage = 1.06% homopolymer indels = 42.25% >>>>>>> Coverage mean coverageData = 0.073X std coverageData = 0.665X There is a 5.93% of reference with a coverageData >= 1X There is a 0.96% of reference with a coverageData >= 2X There is a 0.19% of reference with a coverageData >= 3X There is a 0.05% of reference with a coverageData >= 4X There is a 0.02% of reference with a coverageData >= 5X There is a 0.01% 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 0.01% 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 18997962 0.07622031962760888 1.5447865834681989 chr2 243199373 18222325 0.0749275163632926 0.7382192119103259 chr3 198022430 15258297 0.07705337723610402 0.32991470448157306 chr4 191154276 15016791 0.07855848853729017 0.4025419057735501 chr5 180915260 14122213 0.07805982204044037 0.33298863616078866 chr6 171115067 8954753 0.052331762228746345 0.3243941401949628 chr7 159138663 12808429 0.08048596587744362 0.9631301601205551 chr8 146364022 12270761 0.08383727662252954 0.5919819449287039 chr9 141213431 8601416 0.060910750054646 0.4594028893238377 chr10 135534747 10833961 0.07993493358570257 0.5519697965193398 chr11 135006516 9494848 0.07032881287003954 0.5037718331104576 chr12 133851895 10651165 0.07957425630768993 0.35442399888109877 chr13 115169878 7413856 0.06437322092153297 0.3028668533309239 chr14 107349540 6243283 0.05815845135433277 0.3079823616172775 chr15 102531392 7026637 0.06853156738572319 0.31363093980806783 chr16 90354753 6622380 0.07329310058542245 0.35710667898277704 chr17 81195210 6030640 0.07427334691295213 0.3845175954860473 chr18 78077248 6368081 0.08156128914789619 0.8904383973785208 chr19 59128983 6277495 0.10616612499491154 1.0120773723573009 chr20 63025520 6214292 0.0985996148861604 0.39889610454218205 chr21 48129895 3081858 0.06403209481342105 0.3696190827253269 chr22 51304566 1569634 0.03059443091283532 0.2041482280568419 chrMT 16571 69479 4.192806710518376 3.1572333218995565 chrX 155270560 13173618 0.08484298633301766 0.42659709443285027 chrY 59373566 677328 0.011407904992602264 0.2938038324473874