BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234141.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 = 1,742,365 number of mapped reads = 309,762 (17.78%) number of supplementary alignments = 3,844 (0.22%) number of secondary alignments = 0 number of mapped bases = 18,833,602 bp number of sequenced bases = 18,823,204 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 48,710 duplication rate = 11.36% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 40.1343 >>>>>>> ACTG content number of A's = 4,988,017 bp (26.5%) number of C's = 3,520,070 bp (18.7%) number of T's = 5,918,754 bp (31.44%) number of G's = 4,392,158 bp (23.33%) number of N's = 4,205 bp (0.02%) GC percentage = 42.03% >>>>>>> Mismatches and indels general error rate = 0.0096 number of mismatches = 174,205 number of insertions = 2,485 mapped reads with insertion percentage = 0.78% number of deletions = 5,911 mapped reads with deletion percentage = 1.88% homopolymer indels = 39.42% >>>>>>> Coverage mean coverageData = 0.0061X std coverageData = 0.1461X There is a 0.35% of reference with a coverageData >= 1X There is a 0.12% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.03% 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% 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 1514279 0.006075326889556676 0.17474856044524079 chr2 243199373 1538541 0.006326253974347212 0.1595719032020636 chr3 198022430 1302628 0.006578184097629748 0.14713150297381833 chr4 191154276 990775 0.005183117117401026 0.12624107847423688 chr5 180915260 1258948 0.006958771747612667 0.1462538546588082 chr6 171115067 1072313 0.006266619408798174 0.13614317211335383 chr7 159138663 1039251 0.00653047462136841 0.14002847422989814 chr8 146364022 876735 0.005990099124223301 0.1462796400726564 chr9 141213431 820804 0.005812506602151745 0.1364621262192047 chr10 135534747 1059556 0.007817596767270315 0.15980151883346458 chr11 135006516 760550 0.005633431796728982 0.13475127562153186 chr12 133851895 846025 0.006320605322771112 0.13978586479412697 chr13 115169878 566520 0.004918994530844254 0.167057686046073 chr14 107349540 838287 0.007808948226513127 0.16655214055895554 chr15 102531392 463418 0.0045197669802434755 0.1308069282596928 chr16 90354753 495346 0.005482235118278726 0.13739902670303475 chr17 81195210 546646 0.00673249074668321 0.14099033684414086 chr18 78077248 456758 0.00585007811750742 0.1446448005905712 chr19 59128983 463662 0.00784153517404485 0.16415866133996032 chr20 63025520 450186 0.0071429160759006825 0.14958867055616662 chr21 48129895 267097 0.005549503068726828 0.13303277215255643 chr22 51304566 200072 0.0038996918909712636 0.10068656308324575 chrMT 16571 11639 0.7023716130589585 1.3182251113677879 chrX 155270560 926432 0.005966565715999221 0.13943097434984697 chrY 59373566 67134 0.0011307052030528199 0.051065609052024216