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
A9 F77 I0 R1	41	21.1	946138	88.6%	838278	142.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,184,543	C→A	100%	P1100Q (CCG→CAG)	rpoB →	RNA polymerase subunit beta

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,184,543	0	C	A	100.0%	109.8 / ‑6.7	44	P1100Q (CCG→CAG)	rpoB	RNA polymerase subunit beta
Reads supporting (aligned to +/- strand): ref base C (0/0); major base A (18/25); minor base G (0/1); total (18/26)
Rejected as polymorphism: E-value score below prediction cutoff.
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTC  >  NC_000913/4184404‑4184676

cTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCt                                                                                                                                    >  1:339220/1‑143 (MQ=255)

 aagaggTTGAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTg                                                                                                                                   >  2:81762/5‑143 (MQ=255)

      gTTAAACGCCGTATCCAGCCTGGTGAAAAGATGGCAGGTCGTCACGGTAACAAGGGAGTAATTTCTAAGATCAACTCGACCGCAGAGGTGCCTTACGATGACAACGGTACGCCGGTAGACATAGTACTGAAACAGCAggggga                                                                                                                              >  2:408699/1‑140 (MQ=255)

          aaCGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCg                                                                                                                          >  2:272010/1‑143 (MQ=255)

            cGCCGTATCCGGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGAGTAAGTTCTAAGATCAACCAGATCGAAGCTATGCCTTACGATGAAAACGGTACGCCGGGAGACCTCATACAGCACCAGGTCGGCgccacctc                                                                                                                        >  2:463474/1‑136 (MQ=255)

                            gTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGt                                                                                                        <  1:409100/143‑1 (MQ=255)

                               aCAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATAGATCAg                                                                                                     >  1:38246/1‑143 (MQ=255)

                                 aaGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTAACGTCTCGTATGAACATCGGTCAGAt                                                                                                   >  1:63770/1‑143 (MQ=255)

                                  ggctGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGAGGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATc                                                                                                  <  2:218225/140‑1 (MQ=255)

                                         aGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTTCCGTCTCGTATGAACATCGGTCAGATCCTCGaaa                                                                                           <  1:420096/143‑1 (MQ=255)

                                         aGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCTGATCCTCGaaa                                                                                           >  1:235185/1‑143 (MQ=255)

                                           gacgtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGCCATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATAAACCTCGGTCAGATCCTCGaatgc                                                                                         >  1:428868/3‑140 (MQ=255)

                                                      caCAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATAAACATCGGTCAGATCCTCGAAACCCACCTGGGTAt                                                                              <  2:468264/142‑1 (MQ=255)

                                                        cAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATgg                                                                            <  2:261587/143‑1 (MQ=255)

                                                                   tttCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGt                                                                 >  1:590/1‑143 (MQ=255)

                                                                    ttCTAAGATCCACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTa                                                                <  2:314700/143‑1 (MQ=255)

                                                                       taggggcAACCCGTTCGAAGATATGCCTTACGATGAAACCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCGCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCg                                                             <  1:122798/137‑1 (MQ=255)

                                                                       tAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGGACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGAGCCTCGAAACCCACCTCGGTATGGCTCCGAAAgaaatca                                                             >  2:47925/1‑137 (MQ=255)

                                                                           gtcgaCCGGAACGAAGATATGCCTTAAGATGCGAGCGGTACGCCGGTAGACCGGGTAGTGAACCAGCCGGGCGTACCGTCTCGTATGAACATCGGTCAGATCGGCGAAGCCCACCTGGGTATGGCTGCGAAAGGTATCGGCGa                                                         <  2:216677/139‑1 (MQ=255)

                                                                           aTCAACCCGATCGAAGAGATGCCTTACGATGAACACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGa                                                         <  1:303322/143‑1 (MQ=255)

                                                                           aTCAACCCCATCGAAGATATGCCCTACGATGGAAGCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGa                                                         <  2:215957/143‑1 (MQ=255)

                                                                              aaCCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGCACGGCTGCGAAAGGTATCGGCGACag                                                      >  2:35494/1‑142 (MQ=255)

                                                                                cccGATCGAAGATATGCCTTACGATGAAAACGGTGCGCCGGTAGACATCGTACTGAACCAGCTGAGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGa                                                    <  2:379491/143‑1 (MQ=255)

                                                                                  cGATCGAAGCTATGCCGTACGATGAAACCGGTCCGGCGTACTACATCGTAGTGAACCGGCTGGGCGTCCCGGCTCGTATGAACATCGGTCAGAGCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATc                                                  <  2:205974/143‑1 (MQ=255)

                                                                                   gATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCa                                                 >  2:399124/1‑143 (MQ=255)

                                                                                     tCGAAGATGTGCTTTACGATGAAAACGGTACGCTGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGTACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAAc                                               <  2:270201/143‑1 (MQ=255)

                                                                                        aaGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCAACCGCGTATGGCTGCGAGAGGTATCGGCGACACGATCCACGcc                                            >  1:105602/1‑143 (MQ=255)

                                                                                        aaGATATGCCTTACGATGAAAACGGTACGCCGCGTTACGTCCTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGcc                                            <  2:456395/143‑1 (MQ=255)

                                                                                           acaggCCTTACGATGAGAGCGGTGCGCCGGTAGACGTCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATg                                         <  2:257871/139‑1 (MQ=255)

                                                                                                ccTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGaa                                    >  1:308552/1‑143 (MQ=255)

                                                                                                   tgcGATGAAAACGGTGCGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAca                                 <  1:345716/141‑1 (MQ=255)

                                                                                                    aCGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAAcag                                <  1:389986/143‑1 (MQ=255)

                                                                                                    aCGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGGCTCGTATGAACATCGGTCAGATCCTAGAAACCCAACTGGGTATGGCTGAGAAAGGTATCAGAGACAAGATCAACGCCATGCTGAAAcag                                >  2:357104/1‑143 (MQ=255)

                                                                                                           agaCGGTACGCCGGTAGACACCTTACGGAACCAGCTGGGCGGACCGTCCCGTAGGAACATCGGTCAGATCCCCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaag                         <  1:276685/141‑1 (MQ=255)

                                                                                                               ggTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACCGGATCAACGCCCTGCTGCAACGGCGGCATGACGt                     >  1:80243/1‑143 (MQ=255)

                                                                                                                 tACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCTGATCCTCGAAACCCATCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTcg                   <  2:235185/143‑1 (MQ=255)

                                                                                                                  atgctggTAGACGTTGTACTGAACCATCTGGGCGTACCGTTTCGTATGAACAGCGGTCAGTTCCTCGTCAAACAAATGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTcgc                  <  2:6709/138‑1 (MQ=255)

                                                                                                                  aCGCCGGTAGACCGTGTACTGAATCAGGTGGGCGTACCGTCTCGTATGAAGATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTcgc                  <  2:5211/143‑1 (MQ=255)

                                                                                                                    cccGGTAGACATCGTACTGAACCAGCTGGTCGTATCGTCTTGTATGAACGTCGGTCAGATCCTCGAAACGCACCTGGGTATGGCTGCGAAAGGTAGCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGa                <  2:69566/142‑1 (MQ=255)

                                                                                                                       ggTAGACATCGGACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGCGCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACCAGCTCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAAc             <  2:127275/143‑1 (MQ=255)

                                                                                                                          aGACATCGGACGGAACCAGCCGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTgc          <  1:160572/143‑1 (MQ=255)

                                                                                                                            tcATGGTACTGGACCAGCTGGGCGTCCCGGCGCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTAGGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTgcgc        <  2:152165/142‑1 (MQ=255)

                                                                                                                               tCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAGCCGCAGCCAGAGATTGCGAAACTGAGCGaa     >  1:31185/1‑143 (MQ=255)

                                                                                                                                  tACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTc  <  1:298950/143‑1 (MQ=255)

CTGGCGGTTAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTC  >  NC_000913/4184404‑4184676

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 22 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A