BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716709.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 = 4,838,927 number of mapped reads = 4,560,950 (94.26%) number of supplementary alignments = 89,183 (1.84%) number of secondary alignments = 0 number of mapped bases = 355,413,874 bp number of sequenced bases = 355,277,236 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 456,457 duplication rate = 7.52% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 47.009 >>>>>>> ACTG content number of A's = 91,064,167 bp (25.63%) number of C's = 72,573,518 bp (20.43%) number of T's = 106,620,547 bp (30.01%) number of G's = 85,004,348 bp (23.93%) number of N's = 14,656 bp (0%) GC percentage = 44.35% >>>>>>> Mismatches and indels general error rate = 0.0066 number of mismatches = 2,257,700 number of insertions = 30,012 mapped reads with insertion percentage = 0.65% number of deletions = 66,288 mapped reads with deletion percentage = 1.43% homopolymer indels = 37.85% >>>>>>> Coverage mean coverageData = 0.1148X std coverageData = 0.8513X There is a 7.63% of reference with a coverageData >= 1X There is a 2.19% of reference with a coverageData >= 2X There is a 0.79% of reference with a coverageData >= 3X There is a 0.33% of reference with a coverageData >= 4X There is a 0.15% of reference with a coverageData >= 5X There is a 0.08% of reference with a coverageData >= 6X There is a 0.05% of reference with a coverageData >= 7X There is a 0.03% of reference with a coverageData >= 8X There is a 0.02% 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 0.01% of reference with a coverageData >= 12X There is a 0.01% of reference with a coverageData >= 13X There is a 0.01% of reference with a coverageData >= 14X There is a 0.01% of reference with a coverageData >= 15X There is a 0.01% 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 39302303 0.15768186591599304 1.760094182945272 chr2 243199373 33572283 0.13804428270462688 0.8790985948193293 chr3 198022430 23486799 0.11860676086037324 0.4945263066156539 chr4 191154276 17301858 0.09051253449334296 0.6961312446717274 chr5 180915260 18515511 0.10234355576196282 0.46240359527733077 chr6 171115067 22075241 0.1290081661832853 0.574068605049488 chr7 159138663 22402195 0.14077154211104564 1.229663714602603 chr8 146364022 23424134 0.16004024540949005 0.8936279016749371 chr9 141213431 10683209 0.07565292426044092 0.572750445438833 chr10 135534747 18951303 0.13982615837988763 1.090032983707855 chr11 135006516 15720087 0.11643946874386418 0.7726345703504506 chr12 133851895 12336556 0.09216571793772513 0.4303766464698977 chr13 115169878 6873422 0.05968072658720712 0.3375090939628292 chr14 107349540 6967669 0.06490637034867593 0.4035457000530939 chr15 102531392 7355638 0.07174035050650635 0.3864727627936162 chr16 90354753 10908697 0.12073185568887561 0.55596527193054 chr17 81195210 6285021 0.07740630266243538 0.4817604963686184 chr18 78077248 7457518 0.09551461137564685 0.8874944240632175 chr19 59128983 8964218 0.15160446781234171 1.2353531640648678 chr20 63025520 7667032 0.12164964287482277 0.5503160669677899 chr21 48129895 5414080 0.1124889219060212 0.631197408874385 chr22 51304566 5453017 0.10628716750084194 0.5127611180278561 chrMT 16571 8849 0.5340051897893912 1.131713344810891 chrX 155270560 23213316 0.14950236541943301 0.6104805006975274 chrY 59373566 1073918 0.018087476841124887 0.5773518749297799