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
A3 F50 I2 R1	257	49.9	1554294	99.0%	1538751	150.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	4,184,036	T→C	V931A (GTT→GCT)	rpoB →	RNA polymerase, beta subunit

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,184,036	0	T	C	96.8%	105.3 / ‑3.8	31	V931A (GTT→GCT)	rpoB	RNA polymerase, beta subunit
Reads supporting (aligned to +/- strand): ref base T (0/1); new base C (14/16); total (14/17)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.87e-01

CTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGTTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCTGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGCCGTATCCG  >  NC_000913/4183891‑4184171

cTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAgg                                                                                                                                    >  1:395565/1‑151 (MQ=255)

     tggtAAGGTAACGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCtt                                                                                                                                <  2:490926/150‑1 (MQ=255)

      ggtaaggtaaCGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTa                                                                                                                              <  1:774024/151‑1 (MQ=255)

          aggtaaCGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTcg                                                                                                                          >  2:697974/1‑151 (MQ=255)

          aggtaaCGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTcg                                                                                                                          <  1:427573/151‑1 (MQ=255)

              aaCGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGAt                                                                                                                      <  1:281291/151‑1 (MQ=255)

               aCGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATg                                                                                                                     >  2:591766/1‑151 (MQ=255)

                    gAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTa                                                                                                                <  1:688477/151‑1 (MQ=255)

                            aaaCTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGa                                                                                                        <  1:282617/151‑1 (MQ=255)

                                      gACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTg                                                                                                <  1:45412/149‑1 (MQ=255)

                                         cccAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTg                                                                                           <  2:494528/151‑1 (MQ=255)

                                            agaagaAAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGa                                                                                         >  2:660953/1‑150 (MQ=255)

                                             gaagaaAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGaa                                                                                        >  2:479077/1‑150 (MQ=255)

                                              aagaaAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAAt                                                                                      >  1:105965/1‑151 (MQ=255)

                                               agaaAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGTTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATc                                                                                     <  2:232592/151‑1 (MQ=255)

                                                        gctgcGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATg                                                                            >  2:581817/1‑151 (MQ=255)

                                                         ctgcGTGCGATCTTCGGCGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGCATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGc                                                                           >  2:110513/1‑151 (MQ=255)

                                                           gcgtgcgATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAg                                                                         <  2:285613/151‑1 (MQ=255)

                                                                       cGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCg                                                             <  1:229848/151‑1 (MQ=255)

                                                                          tGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCga                                                            >  2:133983/1‑149 (MQ=255)

                                                                            agaAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCgaaga                                                         >  2:106560/1‑150 (MQ=255)

                                                                                     ctGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCTg                                                 <  1:655037/149‑1 (MQ=255)

                                                                                                gACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCTGTCTGAAGAACTGc                                    <  1:756918/151‑1 (MQ=255)

                                                                                                      tctcTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCTGTCTGAAGAACTGCAGa                                 <  1:106528/148‑1 (MQ=255)

                                                                                                         ctGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCGGCTCAAACAGGCGAAGAAAGACCTGTCTGAAGAACTGCAGATCCTCg                           >  2:520154/1‑151 (MQ=255)

                                                                                                         ctGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCTGTCTGAAGAACTGCAGATcc                              <  1:434918/148‑1 (MQ=255)

                                                                                                             gcgTACCAAACGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAG‑AAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCTGTCTGAAGAACTGCAGATCCTCGAAGCg                      <  1:741933/151‑1 (MQ=255)

                                                                                                                    aaaCGGTGTATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCTGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTg                >  1:435214/1‑151 (MQ=255)

                                                                                                                          tgtATCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCTGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGc          >  1:683179/1‑151 (MQ=255)

                                                                                                                             aTCCGGTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCTGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGCCGt       <  1:17652/151‑1 (MQ=255)

                                                                                                                                  gTACGGTTATCGACGCTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCTGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGCCGTATCCg  >  1:133954/1‑151 (MQ=255)

CTGGTTGGTAAGGTAACGCCGAAAGGTGAAACTCAGCTGACCCCAGAAGAAAAACTGCTGCGTGCGATCTTCGGTGAGAAAGCCTCTGACGTTAAAGACTCTTCTCTGCGCGTACCAAACGGTGTATCCGGTACGGTTATCGACGTTCAGGTCTTTACTCGCGATGGCGTAGAAAAAGACAAACGTGCGCTGGAAATCGAAGAAATGCAGCTCAAACAGGCGAAGAAAGACCTGTCTGAAGAACTGCAGATCCTCGAAGCGGGTCTGTTCAGCCGTATCCG  >  NC_000913/4183891‑4184171

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 31 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 39 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A