BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153340.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 = 74,608,466 number of mapped reads = 73,662,077 (98.73%) number of supplementary alignments = 526,032 (0.71%) number of secondary alignments = 0 number of mapped bases = 7,328,746,563 bp number of sequenced bases = 7,327,765,169 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 32,319,681 duplication rate = 35.19% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 48.8536 >>>>>>> ACTG content number of A's = 1,893,794,433 bp (25.84%) number of C's = 1,767,026,233 bp (24.11%) number of T's = 1,892,820,227 bp (25.83%) number of G's = 1,773,793,314 bp (24.21%) number of N's = 330,962 bp (0%) GC percentage = 48.32% >>>>>>> Mismatches and indels general error rate = 0.0032 number of mismatches = 22,519,858 number of insertions = 610,486 mapped reads with insertion percentage = 0.82% number of deletions = 428,303 mapped reads with deletion percentage = 0.57% homopolymer indels = 47.47% >>>>>>> Coverage mean coverageData = 2.3674X std coverageData = 24.099X There is a 14.5% of reference with a coverageData >= 1X There is a 7.68% of reference with a coverageData >= 2X There is a 5.84% of reference with a coverageData >= 3X There is a 5.14% of reference with a coverageData >= 4X There is a 4.7% of reference with a coverageData >= 5X There is a 4.39% of reference with a coverageData >= 6X There is a 4.13% of reference with a coverageData >= 7X There is a 3.91% of reference with a coverageData >= 8X There is a 3.72% of reference with a coverageData >= 9X There is a 3.56% of reference with a coverageData >= 10X There is a 3.41% of reference with a coverageData >= 11X There is a 3.27% of reference with a coverageData >= 12X There is a 3.14% of reference with a coverageData >= 13X There is a 3.02% of reference with a coverageData >= 14X There is a 2.92% of reference with a coverageData >= 15X There is a 2.81% of reference with a coverageData >= 16X There is a 2.72% of reference with a coverageData >= 17X There is a 2.63% of reference with a coverageData >= 18X There is a 2.55% of reference with a coverageData >= 19X There is a 2.47% of reference with a coverageData >= 20X There is a 2.39% of reference with a coverageData >= 21X There is a 2.32% of reference with a coverageData >= 22X There is a 2.25% of reference with a coverageData >= 23X There is a 2.19% of reference with a coverageData >= 24X There is a 2.13% of reference with a coverageData >= 25X There is a 2.07% of reference with a coverageData >= 26X There is a 2.01% of reference with a coverageData >= 27X There is a 1.96% of reference with a coverageData >= 28X There is a 1.91% of reference with a coverageData >= 29X There is a 1.86% of reference with a coverageData >= 30X There is a 1.81% of reference with a coverageData >= 31X There is a 1.76% of reference with a coverageData >= 32X There is a 1.72% of reference with a coverageData >= 33X There is a 1.68% of reference with a coverageData >= 34X There is a 1.64% of reference with a coverageData >= 35X There is a 1.6% of reference with a coverageData >= 36X There is a 1.56% of reference with a coverageData >= 37X There is a 1.53% of reference with a coverageData >= 38X There is a 1.49% of reference with a coverageData >= 39X There is a 1.46% of reference with a coverageData >= 40X There is a 1.42% of reference with a coverageData >= 41X There is a 1.39% of reference with a coverageData >= 42X There is a 1.36% of reference with a coverageData >= 43X There is a 1.33% of reference with a coverageData >= 44X There is a 1.3% of reference with a coverageData >= 45X There is a 1.28% of reference with a coverageData >= 46X There is a 1.25% of reference with a coverageData >= 47X There is a 1.22% of reference with a coverageData >= 48X There is a 1.2% of reference with a coverageData >= 49X There is a 1.17% of reference with a coverageData >= 50X There is a 1.15% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 812797417 3.2609644611477218 27.16182490332663 chr2 243199373 471349802 1.9381209588891497 15.319863098742319 chr3 198022430 365458930 1.8455431033747036 15.420925021807992 chr4 191154276 269828354 1.4115737280185143 14.521734490248742 chr5 180915260 441558891 2.440694560536242 31.849465729683434 chr6 171115067 282973613 1.6537036624600685 14.024726448450554 chr7 159138663 371138805 2.332172446365218 21.17792709504052 chr8 146364022 412559495 2.818722042224284 52.53580297447578 chr9 141213431 255149132 1.806833317434232 16.446066378569867 chr10 135534747 332757964 2.455148744993046 19.16981333337904 chr11 135006516 344231768 2.5497418806067107 18.667566271886308 chr12 133851895 325396979 2.4310225790975912 19.095031955946354 chr13 115169878 107553271 0.9338663274437089 9.748848360042329 chr14 107349540 166921443 1.5549339382357856 13.677637474754523 chr15 102531392 368368101 3.592734808476998 30.449869803352538 chr16 90354753 282243505 3.1237261530669005 23.670562723309562 chr17 81195210 323526713 3.9845541750554005 27.60261334626051 chr18 78077248 86637049 1.109632462967957 10.585746450221462 chr19 59128983 433916701 7.338477325070854 40.926809511852234 chr20 63025520 170687630 2.7082304120616536 20.766554784668585 chr21 48129895 97911175 2.0343110035872716 43.50372352977656 chr22 51304566 117613744 2.2924615325661266 17.34116623943491 chrMT 16571 972 0.05865668939713958 0.2478685934451662 chrX 155270560 479682266 3.0893317187752785 26.28973483866847 chrY 59373566 8482843 0.1428723853305358 6.351326597819676