BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6237842.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 = 1,687,651 number of mapped reads = 1,130,521 (66.99%) number of supplementary alignments = 8,740 (0.52%) number of secondary alignments = 0 number of mapped bases = 69,883,207 bp number of sequenced bases = 69,855,362 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,921 duplication rate = 7.01% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.2697 >>>>>>> ACTG content number of A's = 18,656,774 bp (26.71%) number of C's = 12,462,257 bp (17.84%) number of T's = 22,828,641 bp (32.68%) number of G's = 15,849,516 bp (22.69%) number of N's = 58,174 bp (0.08%) GC percentage = 40.53% >>>>>>> Mismatches and indels general error rate = 0.0085 number of mismatches = 580,494 number of insertions = 5,771 mapped reads with insertion percentage = 0.51% number of deletions = 16,563 mapped reads with deletion percentage = 1.45% homopolymer indels = 47.93% >>>>>>> Coverage mean coverageData = 0.0226X std coverageData = 0.2518X There is a 1.62% of reference with a coverageData >= 1X There is a 0.41% of reference with a coverageData >= 2X There is a 0.12% of reference with a coverageData >= 3X There is a 0.04% 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% 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 5324647 0.021362622803655924 0.3187321787544356 chr2 243199373 5804291 0.023866389655535832 0.308749699244602 chr3 198022430 4641469 0.023439107377886435 0.2054877795045665 chr4 191154276 5163344 0.027011396804955595 0.24652539118682368 chr5 180915260 4019169 0.02221575449190964 0.19795762347846446 chr6 171115067 4642305 0.02712972668853293 0.23977943108754235 chr7 159138663 3545166 0.022277213677483265 0.25110681503453897 chr8 146364022 3728549 0.025474491265346618 0.2983471019613752 chr9 141213431 3116197 0.022067284803808783 0.2557193779697115 chr10 135534747 3009509 0.022204704451176643 0.32019785312278015 chr11 135006516 3346345 0.024786544376865484 0.2368703193667322 chr12 133851895 3187437 0.02381316304860682 0.20791563630051732 chr13 115169878 2692043 0.023374540693704652 0.20500201603235912 chr14 107349540 1825954 0.017009425471222327 0.18890437901509508 chr15 102531392 1595318 0.015559312800512842 0.16310533449635137 chr16 90354753 2201990 0.02437049437786632 0.24135705305506497 chr17 81195210 1759714 0.021672633151635423 0.20171333074875575 chr18 78077248 1636206 0.02095624579390913 0.37662855676659035 chr19 59128983 1308568 0.0221307374760699 0.27851281459355626 chr20 63025520 1511079 0.02397566890364411 0.21277369704317628 chr21 48129895 1049397 0.021803434227313397 0.22407453578101869 chr22 51304566 625139 0.012184860895227143 0.14378771491801873 chrMT 16571 30777 1.8572807917446141 1.9131628302341777 chrX 155270560 3883747 0.025012771255542583 0.22847337186425443 chrY 59373566 234847 0.003955413424216426 0.1349272909732195