BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153328.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 = 43,914,276 number of mapped reads = 43,417,306 (98.87%) number of supplementary alignments = 364,829 (0.83%) number of secondary alignments = 0 number of mapped bases = 4,236,848,907 bp number of sequenced bases = 4,236,089,547 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,663,185 duplication rate = 29.78% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.2297 >>>>>>> ACTG content number of A's = 1,130,101,775 bp (26.68%) number of C's = 981,743,732 bp (23.18%) number of T's = 1,151,282,932 bp (27.18%) number of G's = 971,226,983 bp (22.93%) number of N's = 1,734,125 bp (0.04%) GC percentage = 46.1% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 12,681,376 number of insertions = 463,322 mapped reads with insertion percentage = 1.05% number of deletions = 356,099 mapped reads with deletion percentage = 0.81% homopolymer indels = 49.3% >>>>>>> Coverage mean coverageData = 1.3686X std coverageData = 12.091X There is a 21.97% of reference with a coverageData >= 1X There is a 10.61% of reference with a coverageData >= 2X There is a 5.95% of reference with a coverageData >= 3X There is a 4.39% of reference with a coverageData >= 4X There is a 3.55% of reference with a coverageData >= 5X There is a 3.09% of reference with a coverageData >= 6X There is a 2.77% of reference with a coverageData >= 7X There is a 2.54% of reference with a coverageData >= 8X There is a 2.35% of reference with a coverageData >= 9X There is a 2.2% of reference with a coverageData >= 10X There is a 2.06% of reference with a coverageData >= 11X There is a 1.95% of reference with a coverageData >= 12X There is a 1.84% of reference with a coverageData >= 13X There is a 1.75% of reference with a coverageData >= 14X There is a 1.67% of reference with a coverageData >= 15X There is a 1.59% of reference with a coverageData >= 16X There is a 1.52% of reference with a coverageData >= 17X There is a 1.45% of reference with a coverageData >= 18X There is a 1.39% of reference with a coverageData >= 19X There is a 1.34% of reference with a coverageData >= 20X There is a 1.29% of reference with a coverageData >= 21X There is a 1.24% of reference with a coverageData >= 22X There is a 1.19% of reference with a coverageData >= 23X There is a 1.15% of reference with a coverageData >= 24X There is a 1.11% of reference with a coverageData >= 25X There is a 1.07% of reference with a coverageData >= 26X There is a 1.03% of reference with a coverageData >= 27X There is a 1% of reference with a coverageData >= 28X There is a 0.97% of reference with a coverageData >= 29X There is a 0.94% of reference with a coverageData >= 30X There is a 0.91% of reference with a coverageData >= 31X There is a 0.88% of reference with a coverageData >= 32X There is a 0.85% of reference with a coverageData >= 33X There is a 0.83% of reference with a coverageData >= 34X There is a 0.8% of reference with a coverageData >= 35X There is a 0.78% of reference with a coverageData >= 36X There is a 0.76% of reference with a coverageData >= 37X There is a 0.74% of reference with a coverageData >= 38X There is a 0.72% of reference with a coverageData >= 39X There is a 0.7% of reference with a coverageData >= 40X There is a 0.68% of reference with a coverageData >= 41X There is a 0.66% of reference with a coverageData >= 42X There is a 0.64% of reference with a coverageData >= 43X There is a 0.63% of reference with a coverageData >= 44X There is a 0.61% of reference with a coverageData >= 45X There is a 0.6% of reference with a coverageData >= 46X There is a 0.58% of reference with a coverageData >= 47X There is a 0.57% of reference with a coverageData >= 48X There is a 0.55% of reference with a coverageData >= 49X There is a 0.54% of reference with a coverageData >= 50X There is a 0.53% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 454268915 1.8225387490609302 15.609003404410835 chr2 243199373 298613733 1.2278556861246512 9.580212922532231 chr3 198022430 218228782 1.10204072336654 9.748715264463963 chr4 191154276 172287497 0.9013007744592645 7.459228332965014 chr5 180915260 268627957 1.4848275209067494 13.191743607334493 chr6 171115067 146256472 0.8547258553216708 7.791864708762856 chr7 159138663 200747579 1.2614632749553765 10.420601681008447 chr8 146364022 257886987 1.761956138373951 19.776791643224865 chr9 141213431 104576665 0.7405574969706671 6.576776486249672 chr10 135534747 198854757 1.4671865436838865 10.486446649428084 chr11 135006516 195759064 1.4499971542114307 10.973546758242174 chr12 133851895 207932031 1.5534485410161731 11.149402489477296 chr13 115169878 53144914 0.4614480359178639 4.100315262728175 chr14 107349540 127318151 1.186014872536948 9.403389352248611 chr15 102531392 190748238 1.8603886505315368 13.194885426314318 chr16 90354753 196735031 2.177362279989853 17.59174010832956 chr17 81195210 156232244 1.9241559200351843 12.092293915245923 chr18 78077248 48411549 0.6200468156869463 5.292709108776333 chr19 59128983 222140407 3.7568785345081954 23.1960038993471 chr20 63025520 99518261 1.5790153099887156 10.796622880004584 chr21 48129895 48043526 0.9982055020066011 12.046121653756913 chr22 51304566 62151640 1.2114251195497883 11.117807668571109 chrMT 16571 7108 0.4289421278136504 1.148633046510333 chrX 155270560 305090503 1.9648960047545394 16.97276826838198 chrY 59373566 3266896 0.0550227352017226 1.989024570663534