BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6004111.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 = 4,319,960 number of mapped reads = 3,179,363 (73.6%) number of supplementary alignments = 24,588 (0.57%) number of secondary alignments = 0 number of mapped bases = 205,889,577 bp number of sequenced bases = 205,777,592 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 399,324 duplication rate = 9.6% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.0789 >>>>>>> ACTG content number of A's = 56,348,418 bp (27.38%) number of C's = 36,997,217 bp (17.98%) number of T's = 67,239,936 bp (32.68%) number of G's = 45,165,861 bp (21.95%) number of N's = 26,160 bp (0.01%) GC percentage = 39.93% >>>>>>> Mismatches and indels general error rate = 0.0106 number of mismatches = 2,148,451 number of insertions = 18,051 mapped reads with insertion percentage = 0.56% number of deletions = 68,648 mapped reads with deletion percentage = 2.13% homopolymer indels = 47.55% >>>>>>> Coverage mean coverageData = 0.0665X std coverageData = 0.6029X There is a 3.65% of reference with a coverageData >= 1X There is a 1.46% of reference with a coverageData >= 2X There is a 0.69% of reference with a coverageData >= 3X There is a 0.35% of reference with a coverageData >= 4X There is a 0.18% of reference with a coverageData >= 5X There is a 0.1% 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% 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 17346846 0.06959599912090089 0.9155528047280079 chr2 243199373 17018471 0.06997744603560306 0.750421659419542 chr3 198022430 13286242 0.06709463165359601 0.43455968894673963 chr4 191154276 15061312 0.07879139465339505 0.4890381917342932 chr5 180915260 12028236 0.06648546949549751 0.43228293418763136 chr6 171115067 12533598 0.07324660662406776 0.5079324698453183 chr7 159138663 12067735 0.07583157211770719 0.8394214909885415 chr8 146364022 12532707 0.0856269650747914 0.787809728407605 chr9 141213431 7450335 0.052759393686851216 0.536660175908821 chr10 135534747 9444660 0.06968441826950841 0.5606657012978807 chr11 135006516 9121026 0.06755989466463974 0.5790022050154896 chr12 133851895 9037114 0.06751577181630487 0.439502511051552 chr13 115169878 6513788 0.056558087176231966 0.3996264192727014 chr14 107349540 5489565 0.05113729411416202 0.39299364511213347 chr15 102531392 5188387 0.05060291193549776 0.37646834772348386 chr16 90354753 5674784 0.06280559474275803 0.44188961802257215 chr17 81195210 5084811 0.06262451935280419 0.4452976398964608 chr18 78077248 5865456 0.07512375436183406 1.0270656745705076 chr19 59128983 3469861 0.05868291358909386 0.6650800730160329 chr20 63025520 4401491 0.06983664712326054 0.4531620555995641 chr21 48129895 2981114 0.061938925900420105 0.4352405611047815 chr22 51304566 2298858 0.044808058604374514 0.34124303866119726 chrMT 16571 189186 11.416691810995111 8.347741338432057 chrX 155270560 11239895 0.07238909294846364 0.4790637804558919 chrY 59373566 564099 0.0095008441972308 0.17942494286390478