BamQC report ----------------------------------- >>>>>>> Input bam file = SRR10525128.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.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 = 559,602 number of mapped reads = 500,471 (89.43%) number of supplementary alignments = 13,616 (2.43%) number of secondary alignments = 0 number of mapped bases = 38,160,253 bp number of sequenced bases = 38,145,065 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 9,962 duplication rate = 1.21% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.632 >>>>>>> ACTG content number of A's = 9,938,966 bp (26.06%) number of C's = 7,693,610 bp (20.17%) number of T's = 11,888,132 bp (31.17%) number of G's = 8,622,856 bp (22.61%) number of N's = 1,501 bp (0%) GC percentage = 42.77% >>>>>>> Mismatches and indels general error rate = 0.0079 number of mismatches = 293,554 number of insertions = 3,678 mapped reads with insertion percentage = 0.73% number of deletions = 8,827 mapped reads with deletion percentage = 1.74% homopolymer indels = 43.4% >>>>>>> Coverage mean coverageData = 0.0123X std coverageData = 0.1613X There is a 1.16% of reference with a coverageData >= 1X There is a 0.05% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% 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 3632546 0.01457386940672858 0.25079885027529264 chr2 243199373 3241446 0.013328348506885336 0.21731876835466804 chr3 198022430 2445106 0.012347621428542212 0.11538196814241597 chr4 191154276 2404187 0.012577207532621452 0.1186221866893396 chr5 180915260 2270395 0.012549494166495407 0.11672532808904522 chr6 171115067 2107457 0.012316022410814356 0.12424353227348706 chr7 159138663 2027107 0.012737991898298153 0.21125188241465906 chr8 146364022 1913529 0.013073766174586266 0.19335465435175303 chr9 141213431 1549424 0.010972214109010637 0.1522964695909981 chr10 135534747 1761980 0.013000208721384193 0.16094955084921903 chr11 135006516 2086292 0.015453268937034121 0.1789756327956572 chr12 133851895 1612146 0.012044252343233542 0.11419228413312689 chr13 115169878 1353488 0.011752100666460721 0.11223763014104395 chr14 107349540 1127138 0.010499700324752207 0.11172312411823569 chr15 102531392 1056192 0.010301157327504147 0.10472196813900025 chr16 90354753 860008 0.009518126843863986 0.10696216741970795 chr17 81195210 1154881 0.014223511460836174 0.13464903969450848 chr18 78077248 990963 0.012692084126735614 0.22474473427495723 chr19 59128983 696539 0.011779992901281592 0.18910425128293673 chr20 63025520 754776 0.011975720311391323 0.11454735026224078 chr21 48129895 494271 0.01026952167670426 0.11069720272280067 chr22 51304566 392417 0.007648773405470382 0.09048643449656556 chrMT 16571 386 0.02329370587170358 0.15083470800338408 chrX 155270560 2145500 0.013817815817757081 0.14136590167269847 chrY 59373566 82079 0.001382416545437072 0.045403395106324795