BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6236127.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 = 1,709,955 number of mapped reads = 1,510,695 (88.35%) number of supplementary alignments = 7,521 (0.44%) number of secondary alignments = 0 number of mapped bases = 99,262,073 bp number of sequenced bases = 99,211,879 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 67,132 duplication rate = 3.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.416 >>>>>>> ACTG content number of A's = 27,362,842 bp (27.58%) number of C's = 17,402,400 bp (17.54%) number of T's = 32,156,618 bp (32.41%) number of G's = 22,234,144 bp (22.41%) number of N's = 55,875 bp (0.06%) GC percentage = 39.95% >>>>>>> Mismatches and indels general error rate = 0.0083 number of mismatches = 806,263 number of insertions = 7,261 mapped reads with insertion percentage = 0.48% number of deletions = 28,856 mapped reads with deletion percentage = 1.89% homopolymer indels = 47.3% >>>>>>> Coverage mean coverageData = 0.0321X std coverageData = 0.3096X There is a 2.75% of reference with a coverageData >= 1X There is a 0.34% of reference with a coverageData >= 2X There is a 0.05% 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% 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 7278646 0.029202117815385502 0.4169317084908169 chr2 243199373 10053178 0.04133718716454092 0.3408690830590578 chr3 198022430 8889307 0.04489040458699552 0.2384426176020994 chr4 191154276 4837725 0.025307961198838158 0.1925608494985782 chr5 180915260 4333122 0.023951113908246325 0.17515933353481303 chr6 171115067 11945087 0.06980733613598153 0.38878769198724167 chr7 159138663 3970413 0.024949392719228764 0.3310667826443905 chr8 146364022 6682376 0.045655864799889145 0.6937413056772286 chr9 141213431 3610446 0.02556729890657497 0.264787986483098 chr10 135534747 4362993 0.03219095543078706 0.2716695532441971 chr11 135006516 2794743 0.020700800841346057 0.21454722192105344 chr12 133851895 3247562 0.024262353551288907 0.18257754121942096 chr13 115169878 5682807 0.04934282382412526 0.2534979334517362 chr14 107349540 3449293 0.03213141854170963 0.2126423387289855 chr15 102531392 1303117 0.012709444147603107 0.13543087598113182 chr16 90354753 3204633 0.03546723214438979 0.22687864903728538 chr17 81195210 2498010 0.030765484811234554 0.23310318978411892 chr18 78077248 1910567 0.024470214421491904 0.447522963919949 chr19 59128983 1890750 0.03197670421627242 0.33664705966581976 chr20 63025520 1981968 0.03144707096426971 0.20326623000137822 chr21 48129895 1071391 0.022260405928581393 0.1790003596050109 chr22 51304566 792206 0.015441237725312792 0.13670227115134306 chrMT 16571 61470 3.7094924868746606 2.994960771227155 chrX 155270560 3202882 0.020627748106273335 0.17628847565209252 chrY 59373566 207381 0.003492816988624197 0.09189019011021161