BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3081053.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP064210/SRP064210.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 = 1,340,395 number of mapped reads = 1,083,040 (80.8%) number of supplementary alignments = 7,262 (0.54%) number of secondary alignments = 0 number of mapped bases = 73,595,737 bp number of sequenced bases = 73,574,470 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 18,148 duplication rate = 1.13% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.9545 >>>>>>> ACTG content number of A's = 22,293,705 bp (30.3%) number of C's = 13,921,079 bp (18.92%) number of T's = 21,258,453 bp (28.89%) number of G's = 16,100,309 bp (21.88%) number of N's = 924 bp (0%) GC percentage = 40.8% >>>>>>> Mismatches and indels general error rate = 0.0077 number of mismatches = 559,054 number of insertions = 4,909 mapped reads with insertion percentage = 0.45% number of deletions = 12,423 mapped reads with deletion percentage = 1.14% homopolymer indels = 45.36% >>>>>>> Coverage mean coverageData = 0.0238X std coverageData = 0.2231X There is a 2.25% of reference with a coverageData >= 1X There is a 0.08% of reference with a coverageData >= 2X There is a 0.01% 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 5880434 0.023592454760624246 0.3607898119628658 chr2 243199373 6245040 0.025678684623911426 0.2354189270270274 chr3 198022430 5042123 0.025462383225981017 0.1634782896110669 chr4 191154276 4859830 0.025423600777834548 0.16693510385087326 chr5 180915260 4552421 0.025163278100476433 0.16346675875759317 chr6 171115067 4365906 0.0255144452007841 0.20563830121717175 chr7 159138663 4089885 0.025700134228223346 0.32958551895081895 chr8 146364022 3779909 0.02582539717308397 0.21268692100158912 chr9 141213431 3124111 0.022123327631633 0.21243645211319806 chr10 135534747 3411810 0.02517295435686319 0.20648630983711502 chr11 135006516 3374462 0.024994808398729435 0.21026568422791397 chr12 133851895 3324703 0.024838669635569972 0.16367402088254632 chr13 115169878 2391750 0.020767148854668405 0.14752704812979192 chr14 107349540 2213054 0.020615402730184033 0.16271021070708208 chr15 102531392 2068868 0.020177898296747987 0.15056227535991926 chr16 90354753 2021407 0.022371894481300836 0.1706742993186544 chr17 81195210 1837629 0.02263223409361217 0.17408900220529452 chr18 78077248 2054458 0.026313145668248963 0.4237105046113641 chr19 59128983 1299082 0.021970308537185564 0.24746262914115047 chr20 63025520 1490394 0.02364746851751481 0.16053344324010296 chr21 48129895 972748 0.020210889718334103 0.15327938878970832 chr22 51304566 761227 0.014837412327004189 0.12558590332797337 chrMT 16571 15798 0.9533522418683242 1.1109976832733395 chrX 155270560 4252341 0.02738665333595757 0.18813109517071472 chrY 59373566 166347 0.002801701349721861 0.06749321839086388