Sample Resequencing Stats

Note: The mutation counts shown below represent unfiltered mutation sets.
ALE, Flask, Isolate Predicted Mutations Mean Coverage Total Reads Percent Mapped Mapped Reads Average Read Length
A13 F69 I0 R1 1426 148.0 5875178 97.4% 5722423 123.7

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA NC_000913 420,941 T→A 28.6% intergenic (+31/‑45) brnQ → / → proY branched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_000913420,9410TA28.6% 42.5 / 21.7 28intergenic (+31/‑45)brnQ/proYbranched‑chain amino acid transport system 2 carrier protein; LIV‑II transport system for Ile, Leu, and Val/proline‑specific permease
Reads supporting (aligned to +/- strand):  ref base T (9/11);  new base A (4/4);  total (13/15)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 4.21e-01

GTTTACCGCTGGCCGAACAAGGTCTGGCGTGGTTAATGCCAACAGTGGTGATGGTGGTTCTGGCCATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCTGCGATGCCCCGTGGTTTTTTATTGTGTTGATGGGTTAGGAATTGATGGAAAGTAAGAACAAGCTAAAGCGTGGGCTAAGTACCCGCCACATACGCTTTATGGCACTGGGTTCAGCAATTGGCACCGGGCTGTTTTACGGTT  >  NC_000913/420795‑421082
                                                                                                                                                  |                                                                                                                                             
gTTTACCGCTGGCCGAACAAGGTCTGGCGTGGTTAATGCCAACAGTGGTGATGGTGGTTCTGGCCATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCTGc                                                                                                                                             <  2:31614/149‑1 (MQ=255)
  ttACCGCTGGCCGAACAAGGTCTGGCGTGGTTAATGCCAACAGTGGTGATGGTGGTTCTGGCCATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCTGCGa                                                                                                                                           <  1:1257043/149‑1 (MQ=255)
      cGCTGGCCGAATAAGGTCTGGCGTGGTTAATGCCAACAGTGGTGATGGTGGTTCTGGCCATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCTGCGATGcc                                                                                                                                       >  1:1087398/1‑149 (MQ=255)
             cGAACAAGGTCTGGCGTGGTTAATGCCAACAGTGGTGATGGTGGTTCTGGCCATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCATCGCAGCCCCGTg                                                                                                                                  <  3:1028241/147‑1 (MQ=255)
             cGAACAAGGTCTGGCGTGGTTAATGCCAACAGTGGTGATGGTGGTTCTGGCCATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCATCGCAGCCCCGTg                                                                                                                                  >  4:1028241/1‑147 (MQ=255)
               aaCAAGGTCTGGCGTGGTTAATGCCAACAGTGGTGATGGTGGTTCTGGCCATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCTGCGATGCCCCGTGGttt                                                                                                                              >  3:185339/1‑149 (MQ=255)
                         ggCGTGGTTAATGCCAACAGTGGTGATGGTGGTTCTGGCCATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCTGCGATGCCCCGTGGTTTTTTATTgtgt                                                                                                                    <  2:1087398/149‑1 (MQ=255)
                                ttAATGCCAACAGTGGTGATGGTGGTTCTGGCCATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCTGCGAt                                                                                                                                          <  2:1418796/120‑1 (MQ=255)
                                ttAATGCCAACAGTGGTGATGGTGGTTCTGGCCATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCTGCGAt                                                                                                                                          >  1:1418796/1‑120 (MQ=255)
                                ttAATGCCAACAGTGGTGATGGTGGTTCTGGCCATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCATCGCAGCCCCGTg                                                                                                                                  <  1:650841/128‑1 (MQ=255)
                                ttAATGCCAACAGTGGTGATGGTGGTTCTGGCCATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCATCGCAGCCCCGTg                                                                                                                                  >  2:650841/1‑128 (MQ=255)
                                                 gATGGTGGTTCTGGCCATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCTGCGATGCCCCGTGGTTTTTTATTGTGTTGATGGGTTAGGAATTGATGGaaa                                                                                            <  4:185339/149‑1 (MQ=255)
                                                                cATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCTGCGATGcc                                                                                                                                       <  2:1313556/91‑1 (MQ=255)
                                                                cATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCTGCGATGcc                                                                                                                                       >  1:1313556/1‑91 (MQ=255)
                                                                cATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCATCGCAGCCCCGTGGt                                                                                                                                >  1:620688/1‑98 (MQ=38)
                                                                cATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCATCGCAGCCCCGTGGt                                                                                                                                <  2:620688/98‑1 (MQ=38)
                                                                              gcgcgGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCATCGCAGCCCCGTGGt                                                                                                                                <  4:1464341/84‑1 (MQ=38)
                                                                              gcgcgGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCATCGCAGCCCCGTGGt                                                                                                                                >  3:1464341/1‑84 (MQ=38)
                                                                                    cAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTAGTTTTAACCACGGGGCTGCGATGCCCCGTGGTTTTTTATTGTGTTGATGGGTTAGGAATTGATGGAAAGTAAGAACAAGCTAAAGCGTGGGCTAAGTACCCGc                                                         <  2:1076614/149‑1 (MQ=255)
                                                                                          gtcAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCTGCGATGCCCCGTGGTTTTTTATTGTGTTGATGGGTTAGGAATTGATGGaaa                                                                                            <  4:480722/108‑1 (MQ=255)
                                                                                          gtcAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCTGCGATGCCCCGTGGTTTTTTATTGTGTTGATGGGTTAGGAATTGATGGaaa                                                                                            >  3:480722/1‑108 (MQ=255)
                                                                                                                                           aCGGGGCTGCGATGCCCCGTGGTTTTTTATTGTGTTGATGGGTTAGGAAtt                                                                                                    <  2:840136/51‑1 (MQ=255)
                                                                                                                                           aCGGGGCTGCGATGCCCCGTGGTTTTTTATTGTGTTGATGGGTTAGGAAtt                                                                                                    >  1:840136/1‑51 (MQ=255)
                                                                                                                                           aCGGGGCTGCGATGCCCCGTGGTTTTTTATTGTGTTGATGGGTTAGGAATTGATGGAAAGTAAGAACAAGCTAAAGCGt                                                                        <  2:722554/79‑1 (MQ=255)
                                                                                                                                           aCGGGGCTGCGATGCCCCGTGGTTTTTTATTGTGTTGATGGGTTAGGAATTGATGGAAAGTAAGAACAAGCTAAAGCGt                                                                        >  1:722554/1‑79 (MQ=255)
                                                                                                                                           aCGGGGCTGCGATGCCCCGTGGTTTTTTATTGTGTTGATGGGTTAGGAATTGATGGAAAGTAAGAACAAGCTAAAGCGTGGGCTAAGTACCCGCCACATACGCTTTATGGCACTGGGTTCAGCAATTGGCACCGGGCTGTTTTACGGtt  >  1:1352314/1‑149 (MQ=255)
                                                                                                                                               ggCTGCGATGCCCCGTGGTTTTTTATTGTGTTGATGGGTTAGGAATTGATGGAAAGTAAGAACAAGCTAAAGCGTgg                                                                      <  3:190633/77‑1 (MQ=255)
                                                                                                                                               ggCTGCGATGCCCCGTGGTTTTTTATTGTGTTGATGGGTTAGGAATTGATGGAAAGTAAGAACAAGCTAAAGCGTgg                                                                      >  4:190633/1‑77 (MQ=255)
                                                                                                                                                  tGCGATGCCCCGTGGTTTTTTATTGTGTTGATGGGTTAGGAATTGATGGAAAGTAAGAACAAGCTAAAGCGTg                                                                       >  1:1060907/1‑73 (MQ=255)
                                                                                                                                                  tGCGATGCCCCGTGGTTTTTTATTGTGTTGATGGGTTAGGAATTGATGGAAAGTAAGAACAAGCTAAAGCGTg                                                                       <  2:1060907/73‑1 (MQ=255)
                                                                                                                                                  |                                                                                                                                             
GTTTACCGCTGGCCGAACAAGGTCTGGCGTGGTTAATGCCAACAGTGGTGATGGTGGTTCTGGCCATTATCTGGGATCGCGCGGCAGGTCGTCAGGTGACCTCCAGCGCTCACTAAATCACTGAACATTTGTTTTAACCACGGGGCTGCGATGCCCCGTGGTTTTTTATTGTGTTGATGGGTTAGGAATTGATGGAAAGTAAGAACAAGCTAAAGCGTGGGCTAAGTACCCGCCACATACGCTTTATGGCACTGGGTTCAGCAATTGGCACCGGGCTGTTTTACGGTT  >  NC_000913/420795‑421082

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 16 ≤ ATCG/ATCG < 31 ≤ ATCG/ATCG < 37 ≤ ATCG/ATCG < 40 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A