BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004020.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 = 2,637,065 number of mapped reads = 2,141,772 (81.22%) number of supplementary alignments = 32,298 (1.22%) number of secondary alignments = 0 number of mapped bases = 139,287,319 bp number of sequenced bases = 139,214,542 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 213,450 duplication rate = 7.74% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.7747 >>>>>>> ACTG content number of A's = 39,163,716 bp (28.13%) number of C's = 25,737,304 bp (18.49%) number of T's = 43,872,008 bp (31.51%) number of G's = 30,395,616 bp (21.83%) number of N's = 45,898 bp (0.03%) GC percentage = 40.32% >>>>>>> Mismatches and indels general error rate = 0.0087 number of mismatches = 1,189,236 number of insertions = 10,239 mapped reads with insertion percentage = 0.47% number of deletions = 43,003 mapped reads with deletion percentage = 1.98% homopolymer indels = 44.02% >>>>>>> Coverage mean coverageData = 0.045X std coverageData = 0.5335X There is a 2.85% of reference with a coverageData >= 1X There is a 0.98% of reference with a coverageData >= 2X There is a 0.36% of reference with a coverageData >= 3X There is a 0.14% of reference with a coverageData >= 4X There is a 0.05% of reference with a coverageData >= 5X There is a 0.02% of reference with a coverageData >= 6X There is a 0.01% of reference with a coverageData >= 7X There is a 0.01% 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 13156044 0.05278239206473231 1.2413561000379612 chr2 243199373 12297848 0.050566939578417416 0.48163621026156195 chr3 198022430 12031790 0.0607597331272018 0.35660829325600957 chr4 191154276 8647093 0.04523619968616344 0.3370636305292126 chr5 180915260 13382429 0.07397070318999072 0.4012276727025025 chr6 171115067 7776114 0.04544377147104176 0.3299721785677977 chr7 159138663 9927878 0.062385078602803144 0.5949715868242962 chr8 146364022 13553349 0.09260027713641267 0.7691108278257569 chr9 141213431 7212899 0.051077995548454595 0.4322594911064556 chr10 135534747 4872244 0.035948301877156266 0.43504695889134387 chr11 135006516 5927469 0.04390505862694805 0.34457830388402455 chr12 133851895 2987088 0.02231636690687121 0.23742265586869998 chr13 115169878 3914412 0.033988157910525875 0.26666546880983294 chr14 107349540 1776009 0.016544169635007287 0.24910226952289752 chr15 102531392 4137889 0.040357288819408595 0.2939540430298415 chr16 90354753 1953058 0.021615442853349397 0.25098496964913514 chr17 81195210 2697854 0.03322676300732519 0.27877107564317494 chr18 78077248 2062484 0.026415941299570395 0.5919471716012203 chr19 59128983 1368655 0.0231469396319568 0.809399170742693 chr20 63025520 2925278 0.04641418269932561 0.33529639482681955 chr21 48129895 1103983 0.02293757341461061 0.24455041556460283 chr22 51304566 654689 0.012760833022152453 0.15550922820260413 chrMT 16571 46171 2.786253092752399 2.76557579671552 chrX 155270560 4547001 0.02928437303246668 0.2685698318088899 chrY 59373566 327591 0.005517455360521886 0.1812977286171832