BamQC report ----------------------------------- >>>>>>> Input bam file = SRR2971292.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP041670/SRP041670.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 = 10,430,343 number of mapped reads = 8,997,264 (86.26%) number of secondary alignments = 0 number of mapped bases = 355,970,728 bp number of sequenced bases = 355,938,333 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 590,790 duplication rate = 5.45% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 42.7873 >>>>>>> ACTG content number of A's = 102,684,201 bp (28.85%) number of C's = 73,295,627 bp (20.59%) number of T's = 104,470,733 bp (29.35%) number of G's = 75,481,969 bp (21.21%) number of N's = 5,803 bp (0%) GC percentage = 41.8% >>>>>>> Mismatches and indels general error rate = 0.0025 number of mismatches = 879,483 number of insertions = 9,147 mapped reads with insertion percentage = 0.1% number of deletions = 24,183 mapped reads with deletion percentage = 0.27% homopolymer indels = 41.88% >>>>>>> Coverage mean coverageData = 0.115X std coverageData = 0.8491X There is a 8.51% of reference with a coverageData >= 1X There is a 2.01% of reference with a coverageData >= 2X There is a 0.54% of reference with a coverageData >= 3X There is a 0.16% of reference with a coverageData >= 4X There is a 0.06% of reference with a coverageData >= 5X There is a 0.03% 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% 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 28088560 0.1126920361815267 1.8209200391424176 chr2 243199373 29924080 0.12304340932655283 0.6594861242193972 chr3 198022430 24136170 0.12188604088940834 0.4500100150625203 chr4 191154276 23572787 0.12331812551240026 0.5054770409504641 chr5 180915260 22147820 0.12242096106210167 0.4565620950482854 chr6 171115067 21379686 0.12494332833940333 0.5560308303806023 chr7 159138663 19424568 0.12206064594120664 1.0820745004919228 chr8 146364022 18241444 0.12463065547624812 1.2585915315137608 chr9 141213431 14748402 0.10444050467125893 0.627903950195295 chr10 135534747 16640053 0.12277333575573797 0.7229378673420238 chr11 135006516 16337704 0.12101418867812276 0.6823958389362519 chr12 133851895 15963871 0.11926518485225779 0.46796026903605986 chr13 115169878 11370687 0.09872969562405892 0.3975849466730091 chr14 107349540 12276624 0.11436121663865537 0.5039530144581593 chr15 102531392 10044975 0.09796975154692136 0.40169665333432925 chr16 90354753 9441633 0.10449514482099242 0.4705652703543705 chr17 81195210 8624054 0.10621382714571463 0.4858153984027649 chr18 78077248 9569729 0.12256744756167635 1.4388909308677744 chr19 59128983 6294607 0.10645552621799702 1.5048708148593621 chr20 63025520 7205107 0.11432046891481419 0.460439324428854 chr21 48129895 4573132 0.09501645494967317 0.47650266598306296 chr22 51304566 3713294 0.07237745661857854 0.33846516476065674 chrMT 16571 56378 3.402208677810633 3.8359146614427444 chrX 155270560 21031100 0.13544808494282495 0.5652729374191129 chrY 59373566 1164263 0.019609113591054984 0.3069142717586073