BamQC report ----------------------------------- >>>>>>> Input bam file = SRR3080687.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 = 2,394,519 number of mapped reads = 2,184,796 (91.24%) number of supplementary alignments = 24,124 (1.01%) number of secondary alignments = 0 number of mapped bases = 157,322,043 bp number of sequenced bases = 157,261,998 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 93,095 duplication rate = 3.5% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.6457 >>>>>>> ACTG content number of A's = 48,560,289 bp (30.88%) number of C's = 29,246,730 bp (18.6%) number of T's = 48,484,272 bp (30.83%) number of G's = 30,968,243 bp (19.69%) number of N's = 2,464 bp (0%) GC percentage = 38.29% >>>>>>> Mismatches and indels general error rate = 0.0081 number of mismatches = 1,251,990 number of insertions = 12,481 mapped reads with insertion percentage = 0.57% number of deletions = 32,922 mapped reads with deletion percentage = 1.49% homopolymer indels = 47.13% >>>>>>> Coverage mean coverageData = 0.0508X std coverageData = 0.5131X There is a 3.54% of reference with a coverageData >= 1X There is a 1.02% of reference with a coverageData >= 2X There is a 0.31% of reference with a coverageData >= 3X There is a 0.1% of reference with a coverageData >= 4X There is a 0.03% 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 13332442 0.053490105446918824 0.6951730820793621 chr2 243199373 13385150 0.05503776524950169 0.3767573214724946 chr3 198022430 10821503 0.0546478648908611 0.3153378987596473 chr4 191154276 10856698 0.05679547550377581 0.3448738705896246 chr5 180915260 10430373 0.057653362132083275 0.3230432531553535 chr6 171115067 9340763 0.05458761267352337 0.330180907612544 chr7 159138663 8001772 0.05028175962493791 0.44265211755300526 chr8 146364022 8385301 0.057290725448908474 1.602918463502965 chr9 141213431 6742684 0.04774817772114042 0.3398920570682746 chr10 135534747 6566341 0.048447657485205624 0.4007499340280543 chr11 135006516 6984857 0.0517371843000526 0.3241649650794897 chr12 133851895 7228214 0.05400158137469776 0.3144769593925342 chr13 115169878 5714792 0.04962054401064834 0.30175531164015457 chr14 107349540 4695424 0.04373958193020669 0.2903892064231192 chr15 102531392 4077208 0.03976546031872853 0.26678608405725185 chr16 90354753 3883502 0.04298060556924991 0.28295870991028094 chr17 81195210 3575602 0.04403710514450298 0.2952495000170162 chr18 78077248 4264525 0.054619304717297416 0.48938389992756487 chr19 59128983 2068485 0.03498259051741174 0.4682983160085401 chr20 63025520 3026109 0.04801402669902605 0.29681792945874447 chr21 48129895 2038974 0.042363981886933265 0.2959174240940426 chr22 51304566 1470236 0.028657020507687366 0.22029051261117683 chrMT 16571 81217 4.901152616015931 3.8423405348914317 chrX 155270560 9959657 0.0641438853572757 0.35107764995985363 chrY 59373566 390214 0.006572183991778429 0.18687647906166185