BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237604.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 = 1,411,819 number of mapped reads = 1,068,119 (75.66%) number of supplementary alignments = 4,847 (0.34%) number of secondary alignments = 0 number of mapped bases = 66,216,878 bp number of sequenced bases = 66,175,017 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 58,362 duplication rate = 3.93% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.3249 >>>>>>> ACTG content number of A's = 17,503,491 bp (26.45%) number of C's = 11,564,253 bp (17.48%) number of T's = 20,886,759 bp (31.56%) number of G's = 16,111,295 bp (24.35%) number of N's = 109,219 bp (0.17%) GC percentage = 41.82% >>>>>>> Mismatches and indels general error rate = 0.0102 number of mismatches = 665,912 number of insertions = 6,285 mapped reads with insertion percentage = 0.58% number of deletions = 25,177 mapped reads with deletion percentage = 2.33% homopolymer indels = 47.7% >>>>>>> Coverage mean coverageData = 0.0214X std coverageData = 0.2423X There is a 1.78% of reference with a coverageData >= 1X There is a 0.22% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% 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 5620452 0.022549400187853494 0.2750850644225352 chr2 243199373 6035330 0.02481638799290819 0.3914927858309326 chr3 198022430 4825916 0.02437055236621427 0.19486829176175488 chr4 191154276 4204109 0.021993277304453288 0.18788986027589488 chr5 180915260 3582727 0.01980334328900724 0.16832290821007959 chr6 171115067 3514159 0.020536818069913153 0.21406032057703273 chr7 159138663 4002350 0.02515007933678568 0.34309536313908984 chr8 146364022 3568593 0.024381627064060867 0.22926669242116446 chr9 141213431 2688585 0.01903915924257941 0.25111853090456066 chr10 135534747 2787137 0.020564003413825683 0.21855458703087893 chr11 135006516 2767761 0.02050094382111157 0.23466188390341494 chr12 133851895 3966880 0.02963633798385895 0.22000685597203426 chr13 115169878 2249679 0.019533571095733903 0.17921572023516677 chr14 107349540 1776637 0.016550019683363337 0.17095768801940092 chr15 102531392 2030231 0.019801067364812526 0.18217264140654457 chr16 90354753 1731001 0.019157830025831622 0.19460455721764178 chr17 81195210 1500054 0.018474661251568904 0.17722176434267803 chr18 78077248 1753948 0.022464265133935048 0.40310427698525886 chr19 59128983 1140446 0.019287427960666938 0.21874232624847398 chr20 63025520 1351324 0.021440902034604394 0.18288600940553001 chr21 48129895 799559 0.016612523256076085 0.16792810556016302 chr22 51304566 642287 0.012519100151826643 0.13737072075284523 chrMT 16571 48739 2.941222617826323 2.5018189905296313 chrX 155270560 3388963 0.021826178768209505 0.1893727764472102 chrY 59373566 240011 0.004042388156372484 0.10436372220016236