BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013186.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 = 2,812,440 number of mapped reads = 2,511,037 (89.28%) number of supplementary alignments = 22,949 (0.82%) number of secondary alignments = 0 number of mapped bases = 164,965,966 bp number of sequenced bases = 164,891,904 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 216,567 duplication rate = 6.62% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2138 >>>>>>> ACTG content number of A's = 44,913,153 bp (27.24%) number of C's = 31,085,325 bp (18.85%) number of T's = 51,302,874 bp (31.11%) number of G's = 37,571,472 bp (22.79%) number of N's = 19,080 bp (0.01%) GC percentage = 41.64% >>>>>>> Mismatches and indels general error rate = 0.0078 number of mismatches = 1,255,767 number of insertions = 11,689 mapped reads with insertion percentage = 0.46% number of deletions = 42,445 mapped reads with deletion percentage = 1.67% homopolymer indels = 46.68% >>>>>>> Coverage mean coverageData = 0.0533X std coverageData = 0.5233X There is a 3.47% of reference with a coverageData >= 1X There is a 1.07% of reference with a coverageData >= 2X There is a 0.38% of reference with a coverageData >= 3X There is a 0.15% of reference with a coverageData >= 4X There is a 0.07% of reference with a coverageData >= 5X There is a 0.03% of reference with a coverageData >= 6X There is a 0.02% 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% 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 9992690 0.04009093321376319 0.5956804123326788 chr2 243199373 11228258 0.046168943042464175 0.5992227772821874 chr3 198022430 8203793 0.04142860483027099 0.2923643500199605 chr4 191154276 22644502 0.1184619171166226 0.5198571472651755 chr5 180915260 7012652 0.03876208120862773 0.2898515482225995 chr6 171115067 6744557 0.03941533097141001 0.3402797398096239 chr7 159138663 6668629 0.041904518199954964 0.717535444149839 chr8 146364022 10059132 0.06872680773967799 0.7151780340178026 chr9 141213431 8446993 0.05981720676413563 0.5056704683553347 chr10 135534747 6022523 0.044435269429469626 0.5381176465618586 chr11 135006516 11810711 0.08748252565824305 0.526658688659229 chr12 133851895 12776321 0.09545117758698897 0.45165264482788076 chr13 115169878 6281462 0.05454084096537812 0.34530831063240963 chr14 107349540 4382010 0.04082001655526423 0.3739156679989353 chr15 102531392 3181509 0.031029608961126755 0.2616258591370213 chr16 90354753 4269911 0.047257181921575284 0.3360719118087433 chr17 81195210 4255298 0.05240823935303573 0.37698782841158407 chr18 78077248 3621206 0.046379785312105265 0.7846040591280082 chr19 59128983 2284544 0.03863661920246455 0.4840311865067383 chr20 63025520 3282106 0.052075825792472635 0.34878613157536126 chr21 48129895 2048026 0.042552056263575895 0.33476141063326836 chr22 51304566 1318636 0.02570211781929897 0.22649664500163114 chrMT 16571 1197419 72.25991189427313 39.928104177561146 chrX 155270560 6854993 0.04414869760243024 0.35049511727749466 chrY 59373566 378085 0.006367901163288727 0.21343475421175825