BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153394.sorted.bam outfile = /mainsd2/zhouyj/SRP013572/SRP013572.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 = 44,870,600 number of mapped reads = 44,516,209 (99.21%) number of supplementary alignments = 246,361 (0.55%) number of secondary alignments = 0 number of mapped bases = 3,781,029,549 bp number of sequenced bases = 3,780,339,750 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 25,324,014 duplication rate = 44.83% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 49.7376 >>>>>>> ACTG content number of A's = 1,006,980,332 bp (26.64%) number of C's = 891,756,020 bp (23.59%) number of T's = 1,037,595,598 bp (27.45%) number of G's = 842,378,652 bp (22.28%) number of N's = 1,629,148 bp (0.04%) GC percentage = 45.87% >>>>>>> Mismatches and indels general error rate = 0.0024 number of mismatches = 8,529,018 number of insertions = 389,368 mapped reads with insertion percentage = 0.87% number of deletions = 334,807 mapped reads with deletion percentage = 0.74% homopolymer indels = 49.54% >>>>>>> Coverage mean coverageData = 1.2214X std coverageData = 14.3119X There is a 16.28% of reference with a coverageData >= 1X There is a 11.7% of reference with a coverageData >= 2X There is a 4.92% of reference with a coverageData >= 3X There is a 3.85% of reference with a coverageData >= 4X There is a 2.52% of reference with a coverageData >= 5X There is a 2.15% of reference with a coverageData >= 6X There is a 1.79% of reference with a coverageData >= 7X There is a 1.63% of reference with a coverageData >= 8X There is a 1.49% of reference with a coverageData >= 9X There is a 1.39% of reference with a coverageData >= 10X There is a 1.31% of reference with a coverageData >= 11X There is a 1.25% of reference with a coverageData >= 12X There is a 1.19% of reference with a coverageData >= 13X There is a 1.14% of reference with a coverageData >= 14X There is a 1.1% of reference with a coverageData >= 15X There is a 1.06% of reference with a coverageData >= 16X There is a 1.02% of reference with a coverageData >= 17X There is a 0.99% of reference with a coverageData >= 18X There is a 0.96% of reference with a coverageData >= 19X There is a 0.93% of reference with a coverageData >= 20X There is a 0.9% of reference with a coverageData >= 21X There is a 0.88% of reference with a coverageData >= 22X There is a 0.85% of reference with a coverageData >= 23X There is a 0.83% of reference with a coverageData >= 24X There is a 0.81% of reference with a coverageData >= 25X There is a 0.79% of reference with a coverageData >= 26X There is a 0.77% of reference with a coverageData >= 27X There is a 0.75% of reference with a coverageData >= 28X There is a 0.73% of reference with a coverageData >= 29X There is a 0.71% of reference with a coverageData >= 30X There is a 0.7% of reference with a coverageData >= 31X There is a 0.68% of reference with a coverageData >= 32X There is a 0.67% of reference with a coverageData >= 33X There is a 0.65% of reference with a coverageData >= 34X There is a 0.64% of reference with a coverageData >= 35X There is a 0.62% of reference with a coverageData >= 36X There is a 0.61% of reference with a coverageData >= 37X There is a 0.6% of reference with a coverageData >= 38X There is a 0.59% of reference with a coverageData >= 39X There is a 0.57% of reference with a coverageData >= 40X There is a 0.56% of reference with a coverageData >= 41X There is a 0.55% of reference with a coverageData >= 42X There is a 0.54% of reference with a coverageData >= 43X There is a 0.53% of reference with a coverageData >= 44X There is a 0.52% of reference with a coverageData >= 45X There is a 0.51% of reference with a coverageData >= 46X There is a 0.5% of reference with a coverageData >= 47X There is a 0.49% of reference with a coverageData >= 48X There is a 0.48% of reference with a coverageData >= 49X There is a 0.48% of reference with a coverageData >= 50X There is a 0.47% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 404670924 1.6235503140431493 17.846662034736276 chr2 243199373 304560876 1.2523094621629638 14.30205656684474 chr3 198022430 224911178 1.1357863753111201 12.486262396879658 chr4 191154276 172445048 0.9021249830686497 10.128955473658346 chr5 180915260 200298453 1.1071396243744172 13.09103490864894 chr6 171115067 217561405 1.2714333624402578 14.631585552879448 chr7 159138663 201624505 1.2669737271828154 17.874873836111817 chr8 146364022 144130201 0.9847379091563909 11.86106502633755 chr9 141213431 160708610 1.1380547081247534 13.425639560386735 chr10 135534747 152492371 1.1251164323197504 11.985236509442313 chr11 135006516 176897601 1.3102893567003833 13.834541446331587 chr12 133851895 203237051 1.5183726087703129 17.95889732085869 chr13 115169878 81659913 0.70903880787301 8.904359682409197 chr14 107349540 118688190 1.105623647758528 13.79807725809884 chr15 102531392 135721585 1.3237076211742058 13.663388096696396 chr16 90354753 124969244 1.383095408384327 14.706328695429997 chr17 81195210 164771308 2.0293230105569036 18.62640364839423 chr18 78077248 76893381 0.9848372345295777 12.35970146127635 chr19 59128983 140967483 2.3840674377910407 23.313200760456905 chr20 63025520 71201628 1.1297269423560488 12.052461517383152 chr21 48129895 41974997 0.8721190229066571 15.03957956946886 chr22 51304566 55362481 1.07909461703662 11.659776136775065 chrMT 16571 6684 0.4033552591877376 1.5248706297452501 chrX 155270560 202183111 1.3021342294379565 14.640200754582747 chrY 59373566 3091321 0.052065611150928684 2.36785247612018