BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6231719.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 = 1,272,180 number of mapped reads = 219,194 (17.23%) number of supplementary alignments = 3,020 (0.24%) number of secondary alignments = 0 number of mapped bases = 13,143,278 bp number of sequenced bases = 13,136,304 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 21,063 duplication rate = 7.48% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 38.3465 >>>>>>> ACTG content number of A's = 3,515,068 bp (26.76%) number of C's = 2,595,754 bp (19.76%) number of T's = 3,999,685 bp (30.45%) number of G's = 3,023,534 bp (23.02%) number of N's = 2,263 bp (0.02%) GC percentage = 42.78% >>>>>>> Mismatches and indels general error rate = 0.0099 number of mismatches = 123,776 number of insertions = 2,296 mapped reads with insertion percentage = 1.02% number of deletions = 3,889 mapped reads with deletion percentage = 1.74% homopolymer indels = 36.2% >>>>>>> Coverage mean coverageData = 0.0042X std coverageData = 0.1055X There is a 0.29% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0% 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 1116491 0.004479391046331636 0.11758878501242137 chr2 243199373 1225508 0.0050391083861881505 0.11740049932544407 chr3 198022430 790868 0.003993830395879901 0.09532484432652089 chr4 191154276 876574 0.004585688682161628 0.10533769111794344 chr5 180915260 802730 0.0044370496994007025 0.10316440096882237 chr6 171115067 616913 0.0036052523650649654 0.09217055743885436 chr7 159138663 602862 0.0037882811670976522 0.09693891643308825 chr8 146364022 632205 0.00431940166279388 0.10336093731044163 chr9 141213431 556028 0.003937500817468276 0.09230339733904411 chr10 135534747 573840 0.004233895828941932 0.10259287147103907 chr11 135006516 626768 0.004642501847836737 0.1090836356659336 chr12 133851895 539886 0.0040334580246323744 0.09692608608935142 chr13 115169878 431881 0.0037499475340244783 0.13882992060410618 chr14 107349540 380284 0.003542483740498562 0.10836202798749096 chr15 102531392 408989 0.0039889149266597295 0.09240869399934333 chr16 90354753 423423 0.0046862282939338015 0.11980681640353381 chr17 81195210 330355 0.004068651340393109 0.10624215116162271 chr18 78077248 272038 0.003484216042040826 0.09676780741315857 chr19 59128983 447478 0.007567828453941107 0.1316389902085986 chr20 63025520 239132 0.0037942090759425706 0.09516673529042101 chr21 48129895 162305 0.0033722284247659383 0.08660640935234355 chr22 51304566 129760 0.0025292095834121273 0.07145505826479896 chrMT 16571 11153 0.6730432683603886 1.3340423421926975 chrX 155270560 883578 0.005690570060415832 0.1170754329406561 chrY 59373566 62229 0.0010480926815141943 0.04783077570057597