BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6013225.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 = 1,305,840 number of mapped reads = 1,119,071 (85.7%) number of supplementary alignments = 8,921 (0.68%) number of secondary alignments = 0 number of mapped bases = 71,999,237 bp number of sequenced bases = 71,967,687 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 41,596 duplication rate = 3.16% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 45.2843 >>>>>>> ACTG content number of A's = 19,187,545 bp (26.66%) number of C's = 12,891,660 bp (17.91%) number of T's = 23,259,063 bp (32.32%) number of G's = 16,628,465 bp (23.11%) number of N's = 954 bp (0%) GC percentage = 41.02% >>>>>>> Mismatches and indels general error rate = 0.0074 number of mismatches = 523,620 number of insertions = 4,667 mapped reads with insertion percentage = 0.41% number of deletions = 18,720 mapped reads with deletion percentage = 1.66% homopolymer indels = 46.59% >>>>>>> Coverage mean coverageData = 0.0233X std coverageData = 0.2183X There is a 2.04% of reference with a coverageData >= 1X There is a 0.23% of reference with a coverageData >= 2X There is a 0.03% of reference with a coverageData >= 3X There is a 0.01% 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 7147534 0.028676093047728054 0.3366122479742521 chr2 243199373 7405149 0.030448881954971158 0.27978845831797006 chr3 198022430 3811008 0.01924533498553674 0.15437408585332926 chr4 191154276 5633860 0.029472843181389256 0.1938649105956492 chr5 180915260 3776605 0.020874994182359188 0.16101969427235485 chr6 171115067 3215364 0.01879065389373339 0.18340135123085624 chr7 159138663 5959437 0.03744807759255839 0.36629677030825597 chr8 146364022 3094361 0.021141541191044888 0.22911817268545742 chr9 141213431 2725874 0.019303220527231577 0.1730116904953324 chr10 135534747 2912520 0.02148910197914045 0.20321419418956496 chr11 135006516 3346743 0.024789492382723217 0.1901668355164766 chr12 133851895 4321193 0.03228339053399281 0.20132000228389837 chr13 115169878 1978022 0.01717482065926995 0.14594323371628848 chr14 107349540 1736191 0.016173250486215405 0.14636641751552015 chr15 102531392 559365 0.005455548677228531 0.08465746105395255 chr16 90354753 2171873 0.024037174889958473 0.17744272443490358 chr17 81195210 1634543 0.02013102743376118 0.16427211474872389 chr18 78077248 1847708 0.023665127131530045 0.2354689367329262 chr19 59128983 1383179 0.023392572133364785 0.24922605797681308 chr20 63025520 1227059 0.019469240396588556 0.1569747169434458 chr21 48129895 913110 0.01897178458419658 0.15618496684257002 chr22 51304566 498571 0.00971786799638847 0.10835279677480218 chrMT 16571 29836 1.800494840383803 1.6911816935184931 chrX 155270560 4521774 0.02912190179516323 0.20377763148015393 chrY 59373566 148358 0.0024987214006987556 0.05962026665823311