BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6234026.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 = 4,702,655 number of mapped reads = 2,865,308 (60.93%) number of supplementary alignments = 24,070 (0.51%) number of secondary alignments = 0 number of mapped bases = 190,743,824 bp number of sequenced bases = 190,654,539 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 361,730 duplication rate = 9.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 39.1251 >>>>>>> ACTG content number of A's = 54,062,594 bp (28.36%) number of C's = 34,909,094 bp (18.31%) number of T's = 61,200,061 bp (32.1%) number of G's = 40,426,793 bp (21.2%) number of N's = 55,997 bp (0.03%) GC percentage = 39.51% >>>>>>> Mismatches and indels general error rate = 0.0084 number of mismatches = 1,574,621 number of insertions = 16,556 mapped reads with insertion percentage = 0.57% number of deletions = 50,061 mapped reads with deletion percentage = 1.73% homopolymer indels = 45.13% >>>>>>> Coverage mean coverageData = 0.0616X std coverageData = 0.822X There is a 3.01% of reference with a coverageData >= 1X There is a 1.4% of reference with a coverageData >= 2X There is a 0.73% of reference with a coverageData >= 3X There is a 0.39% of reference with a coverageData >= 4X There is a 0.21% of reference with a coverageData >= 5X There is a 0.12% of reference with a coverageData >= 6X There is a 0.07% of reference with a coverageData >= 7X There is a 0.04% of reference with a coverageData >= 8X There is a 0.03% of reference with a coverageData >= 9X There is a 0.02% 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% 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 26439427 0.10607567152259974 1.7175436901532948 chr2 243199373 10294525 0.0423295704796081 0.7093681512589711 chr3 198022430 5541103 0.027982198784248836 0.30419144300628415 chr4 191154276 13047078 0.06825417810690251 0.5065660862057271 chr5 180915260 8323318 0.046006721599935796 0.3975403469766695 chr6 171115067 28448155 0.16625160775585004 1.0492518646963578 chr7 159138663 3403315 0.021385846379770077 0.45568571856639595 chr8 146364022 7518463 0.05136824540118199 1.1646426175078677 chr9 141213431 12428786 0.0880141917945468 0.9039557573701216 chr10 135534747 2351158 0.017347271102369048 0.6596047685507747 chr11 135006516 6658583 0.04932045650300316 0.5157434900103135 chr12 133851895 12142173 0.09071349344736583 0.5666127006376974 chr13 115169878 9415441 0.08175263500756683 0.5224591954495565 chr14 107349540 14326589 0.13345738603071797 0.733690369919684 chr15 102531392 1197365 0.011678033201772974 0.18117586129417332 chr16 90354753 7276341 0.08053080505903215 0.5948932361264354 chr17 81195210 2408826 0.029667094893898297 0.30401632843194476 chr18 78077248 2147003 0.0274984461542497 1.6378087596201218 chr19 59128983 3762666 0.0636348844356075 0.9956736508715637 chr20 63025520 8655010 0.13732548339148967 0.6896361982742825 chr21 48129895 1491807 0.030995434334523272 0.4206361903695077 chr22 51304566 1386307 0.027021123227121736 0.2768346955196432 chrMT 16571 25047 1.51149598696518 2.023535808591409 chrX 155270560 1588390 0.010229820772205626 0.3020951800659697 chrY 59373566 466948 0.007864577310380852 0.20847443093061688