BamQC report ----------------------------------- >>>>>>> Input bam file = ERR2093979.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/ERP024468/ERP024468.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 = 348,438 number of mapped reads = 323,976 (92.98%) number of supplementary alignments = 20,916 (6%) number of secondary alignments = 0 number of mapped paired reads (first in pair) = 162,836 number of mapped paired reads (second in pair) = 161,140 number of mapped paired reads (both in pair) = 320,774 number of mapped paired reads (singletons) = 3,202 number of mapped bases = 40,850,162 bp number of sequenced bases = 40,066,985 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 303,707 duplication rate = 49.64% >>>>>>> Insert size mean insert size = 1,095,028.6868 std insert size = 9,570,462.8214 median insert size = 162 >>>>>>> Mapping quality mean mapping quality = 41.6549 >>>>>>> ACTG content number of A's = 10,680,491 bp (26.66%) number of C's = 9,308,060 bp (23.23%) number of T's = 10,013,605 bp (24.99%) number of G's = 10,064,470 bp (25.12%) number of N's = 359 bp (0%) GC percentage = 48.35% >>>>>>> Mismatches and indels general error rate = 0.0366 number of mismatches = 1,421,408 number of insertions = 23,877 mapped reads with insertion percentage = 7.23% number of deletions = 112,444 mapped reads with deletion percentage = 33.27% homopolymer indels = 28.65% >>>>>>> Coverage mean coverageData = 0.0132X std coverageData = 2.4435X There is a 0.02% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0.01% 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 0.01% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% of reference with a coverageData >= 8X There is a 0.01% of reference with a coverageData >= 9X There is a 0.01% of reference with a coverageData >= 10X There is a 0.01% of reference with a coverageData >= 11X There is a 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% of reference with a coverageData >= 16X There is a 0.01% of reference with a coverageData >= 17X There is a 0.01% of reference with a coverageData >= 18X There is a 0.01% of reference with a coverageData >= 19X There is a 0.01% of reference with a coverageData >= 20X There is a 0.01% of reference with a coverageData >= 21X There is a 0.01% of reference with a coverageData >= 22X There is a 0.01% of reference with a coverageData >= 23X There is a 0.01% of reference with a coverageData >= 24X There is a 0.01% of reference with a coverageData >= 25X There is a 0.01% of reference with a coverageData >= 26X There is a 0.01% of reference with a coverageData >= 27X There is a 0.01% of reference with a coverageData >= 28X There is a 0.01% of reference with a coverageData >= 29X There is a 0.01% of reference with a coverageData >= 30X There is a 0.01% of reference with a coverageData >= 31X There is a 0.01% of reference with a coverageData >= 32X There is a 0.01% of reference with a coverageData >= 33X There is a 0.01% of reference with a coverageData >= 34X There is a 0.01% of reference with a coverageData >= 35X There is a 0.01% of reference with a coverageData >= 36X There is a 0.01% of reference with a coverageData >= 37X There is a 0.01% of reference with a coverageData >= 38X There is a 0.01% of reference with a coverageData >= 39X There is a 0.01% of reference with a coverageData >= 40X There is a 0.01% of reference with a coverageData >= 41X There is a 0.01% of reference with a coverageData >= 42X There is a 0.01% of reference with a coverageData >= 43X There is a 0.01% 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 825543 0.0033121000729623056 1.0230356064433064 chr2 243199373 1797577 0.007391371851933187 2.304896823125235 chr3 198022430 711128 0.0035911487400694963 1.1292234342427465 chr4 191154276 865428 0.004527379758954489 1.3632270804228175 chr5 180915260 287833 0.00159098243011673 0.8821557967499006 chr6 171115067 723905 0.004230515831782364 1.2410028581384434 chr7 159138663 970687 0.006099630232535006 1.7911712009713359 chr8 146364022 548268 0.0037459205650962504 1.1266770071465906 chr9 141213431 625157 0.004427036405623485 1.3377246855119271 chr10 135534747 729884 0.005385216825615944 1.4947339038703606 chr11 135006516 731810 0.005420553182781193 1.3861265285652968 chr12 133851895 1020135 0.007621371367211499 1.8956431157047537 chr13 115169878 802966 0.006972013984420475 1.8791644173412243 chr14 107349540 169729 0.0015810873525866995 0.5559012473705256 chr15 102531392 718538 0.00700798054121805 1.9402326397847283 chr16 90354753 269989 0.0029880995856410566 0.860258461847679 chr17 81195210 913101 0.011245749595327113 2.566695853546795 chr18 78077248 230100 0.0029470813315551287 0.7450542136923619 chr19 59128983 177186 0.0029966015143537985 0.852360683761367 chr20 63025520 270345 0.004289452907330237 1.2259788629141377 chr21 48129895 114365 0.0023761738935852653 0.43290956449835877 chr22 51304566 85820 0.001672755598400345 0.3854417978277653 chrMT 16571 693602 41.85637559592058 170.14864048240523 chrX 155270560 25995096 0.16741806044880628 8.674513950273308 chrY 59373566 571970 0.00963341160946944 1.3295911688911204