BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238256.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 = 1,107,107 number of mapped reads = 600,603 (54.25%) number of supplementary alignments = 7,408 (0.67%) number of secondary alignments = 0 number of mapped bases = 37,264,441 bp number of sequenced bases = 37,247,748 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 57,685 duplication rate = 7.35% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 43.9668 >>>>>>> ACTG content number of A's = 10,501,717 bp (28.19%) number of C's = 7,259,809 bp (19.49%) number of T's = 11,355,747 bp (30.49%) number of G's = 8,121,768 bp (21.8%) number of N's = 8,707 bp (0.02%) GC percentage = 41.3% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 362,779 number of insertions = 3,066 mapped reads with insertion percentage = 0.5% number of deletions = 10,028 mapped reads with deletion percentage = 1.65% homopolymer indels = 45.17% >>>>>>> Coverage mean coverageData = 0.012X std coverageData = 0.2007X There is a 0.82% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.08% of reference with a coverageData >= 3X There is a 0.03% 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 3127323 0.012546901538110913 0.26796471309612996 chr2 243199373 2516724 0.010348398389990915 0.20581603409134072 chr3 198022430 2196914 0.011094268462416101 0.1517271386942911 chr4 191154276 3342926 0.01748810473902242 0.26766371275656653 chr5 180915260 1884786 0.010418059814302012 0.15163990362416163 chr6 171115067 2476817 0.014474569910316547 0.19131255381477333 chr7 159138663 2041739 0.012829936870840745 0.2012698286680673 chr8 146364022 2164298 0.014787090231778408 0.20342741027052066 chr9 141213431 1458572 0.010328847544253776 0.17455190289998995 chr10 135534747 1671727 0.012334305681774725 0.20633023195059572 chr11 135006516 1522614 0.011278077866997175 0.16277190806404065 chr12 133851895 1427445 0.010664361531825903 0.1480432016261478 chr13 115169878 1088630 0.009452384763314588 0.14989020310880988 chr14 107349540 1252047 0.011663273079698338 0.2334282073960318 chr15 102531392 933486 0.009104392145578205 0.24980979848974164 chr16 90354753 1352464 0.014968376926446803 0.18377566980038937 chr17 81195210 749969 0.009236616297931861 0.1456660860028345 chr18 78077248 1254708 0.01607008484725281 0.2886223860448393 chr19 59128983 588431 0.009951650952630117 0.21798628450796212 chr20 63025520 792828 0.012579475742524616 0.1600502874890364 chr21 48129895 552095 0.011470937137926438 0.1552750125980112 chr22 51304566 326850 0.006370777992742401 0.1076000687983577 chrMT 16571 22552 1.3609317482348682 2.0671178082919686 chrX 155270560 2389556 0.015389626984020667 0.19238127538517924 chrY 59373566 128940 0.0021716735019756098 0.09822459574303327