BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3084972.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 = 2,765,097 number of mapped reads = 2,513,474 (90.9%) number of supplementary alignments = 24,375 (0.88%) number of secondary alignments = 0 number of mapped bases = 174,231,213 bp number of sequenced bases = 174,160,585 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 100,506 duplication rate = 2.58% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 46.5725 >>>>>>> ACTG content number of A's = 51,361,780 bp (29.49%) number of C's = 32,264,910 bp (18.53%) number of T's = 54,363,460 bp (31.21%) number of G's = 36,145,501 bp (20.75%) number of N's = 24,934 bp (0.01%) GC percentage = 39.28% >>>>>>> Mismatches and indels general error rate = 0.0089 number of mismatches = 1,524,410 number of insertions = 15,192 mapped reads with insertion percentage = 0.6% number of deletions = 42,902 mapped reads with deletion percentage = 1.69% homopolymer indels = 46.85% >>>>>>> Coverage mean coverageData = 0.0563X std coverageData = 0.6138X There is a 4.9% of reference with a coverageData >= 1X There is a 0.49% of reference with a coverageData >= 2X There is a 0.06% of reference with a coverageData >= 3X There is a 0.02% of reference with a coverageData >= 4X There is a 0.01% of reference with a coverageData >= 5X There is a 0.01% of reference with a coverageData >= 6X There is a 0.01% 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 14228207 0.057083938017550614 1.259682029184645 chr2 243199373 14592356 0.06000161850746219 0.6236972994300969 chr3 198022430 11610602 0.05863276195529971 0.3005867419779114 chr4 191154276 11469249 0.05999996045079316 0.28079729543648374 chr5 180915260 11959753 0.06610693315754569 0.2892431679870533 chr6 171115067 10309753 0.060250410327689026 0.41317961397856506 chr7 159138663 9536974 0.059928705068987544 0.49765385193831563 chr8 146364022 8980083 0.061354442692207516 1.0287279844542092 chr9 141213431 6740706 0.04773417055492406 0.5391580215862818 chr10 135534747 8391494 0.06191396808377117 0.8372636778315267 chr11 135006516 8257137 0.06116102573893545 0.48973773923179953 chr12 133851895 8223031 0.06143380338395658 0.284603004256181 chr13 115169878 5864015 0.050916221340444594 0.24542105640314338 chr14 107349540 4936193 0.04598243271466278 0.27597226026860033 chr15 102531392 4640618 0.045260460328091515 0.23546142658932348 chr16 90354753 4839090 0.05355656276322287 0.3763407809438881 chr17 81195210 4150111 0.051112756528371564 0.3359155139360529 chr18 78077248 4136196 0.05297568889723162 1.1360567125303327 chr19 59128983 2951461 0.049915639509646226 0.9049229900728923 chr20 63025520 3362721 0.05335491083611845 0.2802310415605437 chr21 48129895 2241599 0.04657394328410648 0.2671926256643874 chr22 51304566 1597885 0.03114508365590696 0.1925965190236974 chrMT 16571 29911 1.8050208195039528 1.6389599975098812 chrX 155270560 10785867 0.06946498421851509 0.3732025964785426 chrY 59373566 396201 0.006673020111340458 0.130719262829031