BamQC report ----------------------------------- >>>>>>> Input bam file = SRR1153322.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 = 44,447,490 number of mapped reads = 43,842,672 (98.64%) number of supplementary alignments = 421,757 (0.95%) number of secondary alignments = 0 number of mapped bases = 4,286,017,595 bp number of sequenced bases = 4,285,204,332 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 19,471,510 duplication rate = 29.17% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 50.1724 >>>>>>> ACTG content number of A's = 1,142,254,333 bp (26.66%) number of C's = 994,220,746 bp (23.2%) number of T's = 1,160,135,771 bp (27.07%) number of G's = 986,873,382 bp (23.03%) number of N's = 1,720,100 bp (0.04%) GC percentage = 46.23% >>>>>>> Mismatches and indels general error rate = 0.0035 number of mismatches = 14,183,569 number of insertions = 485,545 mapped reads with insertion percentage = 1.09% number of deletions = 377,970 mapped reads with deletion percentage = 0.85% homopolymer indels = 49.24% >>>>>>> Coverage mean coverageData = 1.3845X std coverageData = 11.7796X There is a 22.68% of reference with a coverageData >= 1X There is a 10.91% of reference with a coverageData >= 2X There is a 6.22% of reference with a coverageData >= 3X There is a 4.6% of reference with a coverageData >= 4X There is a 3.72% of reference with a coverageData >= 5X There is a 3.24% of reference with a coverageData >= 6X There is a 2.9% of reference with a coverageData >= 7X There is a 2.65% of reference with a coverageData >= 8X There is a 2.45% of reference with a coverageData >= 9X There is a 2.28% of reference with a coverageData >= 10X There is a 2.14% of reference with a coverageData >= 11X There is a 2.01% of reference with a coverageData >= 12X There is a 1.9% of reference with a coverageData >= 13X There is a 1.8% of reference with a coverageData >= 14X There is a 1.71% of reference with a coverageData >= 15X There is a 1.63% of reference with a coverageData >= 16X There is a 1.55% of reference with a coverageData >= 17X There is a 1.48% of reference with a coverageData >= 18X There is a 1.42% of reference with a coverageData >= 19X There is a 1.36% of reference with a coverageData >= 20X There is a 1.3% of reference with a coverageData >= 21X There is a 1.25% of reference with a coverageData >= 22X There is a 1.2% of reference with a coverageData >= 23X There is a 1.16% of reference with a coverageData >= 24X There is a 1.12% of reference with a coverageData >= 25X There is a 1.08% of reference with a coverageData >= 26X There is a 1.04% 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 0.73% of reference with a coverageData >= 38X There is a 0.71% of reference with a coverageData >= 39X There is a 0.69% of reference with a coverageData >= 40X There is a 0.67% 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 0.62% of reference with a coverageData >= 44X There is a 0.61% of reference with a coverageData >= 45X There is a 0.59% of reference with a coverageData >= 46X There is a 0.58% of reference with a coverageData >= 47X There is a 0.56% of reference with a coverageData >= 48X There is a 0.55% of reference with a coverageData >= 49X There is a 0.53% of reference with a coverageData >= 50X There is a 0.52% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 475502401 1.9077280493515802 17.281032117855748 chr2 243199373 297843776 1.2246897363505949 8.876641485606461 chr3 198022430 232318887 1.1731948092950883 8.568230171429938 chr4 191154276 163580809 0.8557528108866369 6.820983827321227 chr5 180915260 268626205 1.4848178368148712 12.375324429948838 chr6 171115067 146713786 0.857398407821095 7.08632640231579 chr7 159138663 201055703 1.2633994732002995 10.255200059088724 chr8 146364022 256054949 1.749439141539852 18.09989554318129 chr9 141213431 105019884 0.7436961431806016 6.127665447653 chr10 135534747 203064137 1.498244114477891 10.191588501934591 chr11 135006516 198774641 1.4723336835090242 9.95713210595105 chr12 133851895 210645271 1.5737190048747536 11.46767743870783 chr13 115169878 49299894 0.42806239666243284 3.8722792788273153 chr14 107349540 117365868 1.0933057375001327 8.561830780143698 chr15 102531392 197099658 1.922334751877747 13.435837637027255 chr16 90354753 206193039 2.282038654900645 17.772362219899257 chr17 81195210 171491868 2.1120934104364038 13.074939824993157 chr18 78077248 43194885 0.5532326779755352 5.016356513031595 chr19 59128983 233631795 3.951222956092446 23.537323502789775 chr20 63025520 100528881 1.595050401805491 10.823824772305707 chr21 48129895 43501841 0.9038424247549263 9.256784580982645 chr22 51304566 58948953 1.149000129929956 8.901260584203987 chrMT 16571 6093 0.3676905437209583 0.9503431114107022 chrX 155270560 302312634 1.9470054980158504 15.847407431765479 chrY 59373566 3241737 0.05459899444139838 1.8705615416170982