BamQC report ----------------------------------- >>>>>>> Input bam file = SRR6238300.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 = 1,861,842 number of mapped reads = 61,244 (3.29%) number of supplementary alignments = 650 (0.03%) number of secondary alignments = 0 number of mapped bases = 3,494,267 bp number of sequenced bases = 3,492,244 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 4,501 duplication rate = 3.08% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 36.897 >>>>>>> ACTG content number of A's = 986,671 bp (28.25%) number of C's = 601,800 bp (17.23%) number of T's = 1,167,795 bp (33.44%) number of G's = 735,442 bp (21.06%) number of N's = 536 bp (0.02%) GC percentage = 38.29% >>>>>>> Mismatches and indels general error rate = 0.0139 number of mismatches = 47,703 number of insertions = 455 mapped reads with insertion percentage = 0.72% number of deletions = 1,384 mapped reads with deletion percentage = 2.23% homopolymer indels = 31.48% >>>>>>> Coverage mean coverageData = 0.0011X std coverageData = 0.0924X There is a 0.1% of reference with a coverageData >= 1X There is a 0.01% of reference with a coverageData >= 2X There is a 0% of reference with a coverageData >= 3X There is a 0% 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 297793 0.0011947532921091498 0.08261175923379845 chr2 243199373 324443 0.001334061827536044 0.26763046937739976 chr3 198022430 218354 0.0011026730658744062 0.04223128849986979 chr4 191154276 224738 0.0011756891067401494 0.04085477557035864 chr5 180915260 212486 0.0011745056774094126 0.048830677116520574 chr6 171115067 210444 0.0012298391000250142 0.10720276591025889 chr7 159138663 206369 0.0012967873181138892 0.08775794884855345 chr8 146364022 187397 0.0012803488004722908 0.050182922452233526 chr9 141213431 128414 9.093610932801427E-4 0.03752321678638101 chr10 135534747 154241 0.0011380181349362759 0.04022954554533838 chr11 135006516 159009 0.001177787596563117 0.039585230433288314 chr12 133851895 156963 0.001172661769188998 0.04305460438828798 chr13 115169878 91296 7.92707273684878E-4 0.04518837775169851 chr14 107349540 100845 9.394078446912767E-4 0.03436751402165174 chr15 102531392 107422 0.0010476986404319957 0.05182430012614709 chr16 90354753 95504 0.001056989221142578 0.03844387469093663 chr17 81195210 90557 0.001115299781846737 0.038936183009418236 chr18 78077248 83973 0.0010755117803332413 0.05038221380145841 chr19 59128983 65498 0.0011077139615271246 0.03805520579943035 chr20 63025520 76792 0.0012184270752545953 0.038809281266936016 chr21 48129895 42030 8.732618261477612E-4 0.033280204540085664 chr22 51304566 45334 8.836250559063301E-4 0.03334177773449888 chrMT 16571 1112 0.06710518375475227 0.24999516697998522 chrX 155270560 199417 0.0012843194485805938 0.04484626308183155 chrY 59373566 13836 2.330329965358658E-4 0.027357085216777526