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
A2 F50 I1 R1 170 39.5 1266514 99.2% 1256381 150.0

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation annotation gene description
RA NC_000913 4,465,700 A→G W161R (TGG→CGG)  treB ← trehalose‑specific PTS enzyme: IIB and IIC component

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*NC_0009134,465,7000AG96.3% 87.3 / NA 27W161R (TGG→CGG) treBtrehalose‑specific PTS enzyme: IIB and IIC component
Reads supporting (aligned to +/- strand):  ref base A (0/0);  major base G (13/13);  minor base C (0/1);  total (13/14)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

GATAAGCGTTCATCAGCTGTGGAGAAACCAGTGTCACGCCAAGCACGATACCAAGGATCGGCGTGCCGCCCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCAC‑ATTGCGAAAACCGAGGATCAAACCGCCGCTAATCAACGCGGGCAGCAACGGGAAGA  >  NC_000913/4465562‑4465837
                                                                                                                                          |                                                                                                                                           
gATAAGCGTTCATCAGCTGTGGAGAAACCAGTGTCACGCCAAGCACGATACCAAGGATCGGCGTGCCGCCCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑a                                                                                                                                <  1:395885/151‑1 (MQ=255)
 aTAAGCGTTCATCAGCTGTGGAGAAACCAGTGTCACGCCAAGCACGATACCAAGGATCGGCGTGCCGCCCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGGAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGt                                                                                                                                  >  1:583967/1‑149 (MQ=255)
       gTTCATCAGCTGTGGAGAAACCAGTGTCACGCCAAGCACGATACCAAGGATCGGCGTGCCGCCCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGtt                                                                                                                         <  2:543273/151‑1 (MQ=255)
          catcaGCTGTGGAGAAACCAGTGTCACGCCAAGCACGATACCAAGGATCGGCGTGCCGCCCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGc                                                                                                                      <  1:352972/151‑1 (MQ=255)
                    ggAGAAACCAGTGTCACGCCAAGCACGATACCAAGGATCGGCGTGCCGCCCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAggg                                                                                                             <  2:232399/150‑1 (MQ=255)
                      agaAACCAGTGTCACGCCAAGCACGATACCAAGGATCGGCGTGCCGCCCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTAc                                                                                                          <  2:35385/151‑1 (MQ=255)
                        aaaCCAGTGTCACGCCAAGCACGATACCAAGGATCGGCGTGCCGCCCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACa                                                                                                         <  1:481341/150‑1 (MQ=255)
                            cAGTGTCACGCCAAGCACGATACCAAGGATCGGCGTGCCGCCCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACATTTgc                                                                                                    <  1:71902/151‑1 (MQ=255)
                             aGTGTCACGCCAAGCACGATACCAAGGATCGGCGTGCCGCCCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGGAGAAGAAAATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACATTTgc                                                                                                    >  2:631585/1‑150 (MQ=255)
                                        aaGCACGATACCAAGGATCGGCGTGCCGCCCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTg                                                                                         >  2:268743/1‑150 (MQ=255)
                                                    aaGGATCGGCGTGCCGCCCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATg                                                                            <  2:140132/151‑1 (MQ=255)
                                                          cGGCGTGCCGCCCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCaa                                                                       <  2:291835/150‑1 (MQ=255)
                                                                       aTTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCAC‑At                                                        >  2:397057/1‑151 (MQ=255)
                                                                         ttttttCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAAGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCAC‑ATTg                                                      >  1:628493/1‑151 (MQ=255)
                                                                               cACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCAC‑ATTGCGaaa                                                 >  1:127499/1‑150 (MQ=255)
                                                                                aCCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCAC‑ATTGCGAAAAc                                               <  2:311943/151‑1 (MQ=255)
                                                                                      gACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCAC‑ATTGCGAAAACCGAgg                                          <  1:517361/150‑1 (MQ=255)
                                                                                                    gaccgGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCAC‑ATTGCGAAAACCGAGGATCAAACCGCCGCt                            >  2:346654/1‑150 (MQ=255)
                                                                                                     accgGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCCGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCAC‑ATTGCGAAAACCGAGGATCAAACCGCCGCTa                           >  1:201475/1‑150 (MQ=255)
                                                                                                       cgGCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCAC‑ATTGCGAAAACCGAGGATCAAACCGCCGCTAATc                        >  2:562100/1‑151 (MQ=255)
                                                                                                        ggCAGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCAC‑ATTGCGAAAACCGAGGATCAAACCGCCGCTAATc                        >  2:297862/1‑150 (MQ=255)
                                                                                                           aGGTAGAAGAAGATCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCAC‑ATTGCGAAAACCGAGGATCAAACCGCCGCTAATCAAcg                    >  1:83747/1‑151 (MQ=255)
                                                                                                               agaagaagaTCGCTTCACCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCAC‑ATTGCGAAAACCGAGGATCAAACCGCCGCTAATCAACGCggg                >  2:215934/1‑151 (MQ=255)
                                                                                                                 aagaagaTCGCTTCACCGATCAACCGCAAAAAATCGA‑AGATCGTTTGAGGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTTCTCATGGAAAAATCGCCGATCAC‑ATTGCGAAACCCGAGGATCAAACCGCCGCTAATCAACGCGGgca              <  1:474751/151‑1 (MQ=255)
                                                                                                                 aaaaagcTCGCTTCCCCGAT‑AACCCCCAAAAAGCGTGAGTTCGTTGGAAGGAAGGGGTAAATTGGCGCGGGGGTCCTCCCGTGCCTGATGGGCAAGACCCCG‑TCACTATTGGAAAAACCAAGAACCAAACCGCCGCTAATCAACGCGGgca              <  1:328944/148‑1 (MQ=255)
                                                                                                                              cACCGATCAACCGAAGAAAATCGT‑AGATCGTTTGCAGGGAGGGTTACTTTGGCGCCAGCGTCTGACGGTTGCTCAGGGGAAAATCGCCGATCAC‑ATGGCAAAACCCGAGGATCAAACCGCCGCTAATCAACGCGGGCAGCAACGGgaaga  <  1:113713/150‑1 (MQ=255)
                                                                                                                               aCCGATCAACCGCAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCAC‑ATTGCGAAAACCGAGGATCAAACCGCCGCTAATCAACGCGGGCAGCAACGGgaaga  >  2:47906/1‑149 (MQ=255)
                                                                                                                                          |                                                                                                                                           
GATAAGCGTTCATCAGCTGTGGAGAAACCAGTGTCACGCCAAGCACGATACCAAGGATCGGCGTGCCGCCCATTTTTTTCACCGCTGACCAGCAAATACCGACCGGCAGGTAGAAGAAGATCGCTTCACCGATCAACCACAGAAAATCGT‑AGATCGTTTGCAGGGAAGGGTACATTTGCGCCAGCGTCTGACCGTTGCTCATGGGCAAATCGCCGATCAC‑ATTGCGAAAACCGAGGATCAAACCGCCGCTAATCAACGCGGGCAGCAACGGGAAGA  >  NC_000913/4465562‑4465837

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 14 ≤ ATCG/ATCG < 19 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG < 39 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A