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 F44 I0 R1	30	22.2	989614	86.8%	858984	142.7

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%	97.7 / ‑6.7	42	P1100Q (CCG→CAG)	rpoB	RNA polymerase subunit beta
Reads supporting (aligned to +/- strand): ref base C (1/0); new base A (25/15); total (26/16)
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.

TAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  NC_000913/4184412‑4184681

tAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTAc                                                                                                                                 >  1:342346/1‑143 (MQ=255)

    cGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCAAAGATCAACCCGATCGAAGATATGCCTTAACATGAAAACGGTACGCCGGAAGACATCGTACTGCAACAGCTCGGCGGAccatg                                                                                                                             >  2:289304/1‑140 (MQ=255)

           tCCAGACGGGTGAAAAGATGGCAGGTCGTCACGGTAACAAGGGTTTCATAACAAAAATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATg                                                                                                                      <  1:209184/143‑1 (MQ=255)

              aGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGCGTAATTTCTAATATCAACCCAATCAAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTCGGCGTACCGTCTCGTATGCAc                                                                                                                   >  1:466902/1‑143 (MQ=255)

                cggtggtaCAAGAGGGCAGGTCGTCACGGTAACAAGGTTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACAt                                                                                                                 <  2:90311/136‑1 (MQ=255)

                ccTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACCGAACCCGCTGCGCGTACCGCCTCGTCAGAACAt                                                                                                                 >  2:58615/1‑143 (MQ=255)

                         aaGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCCACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCAGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGGATGAACATCGGTCAGAt                                                                                                        >  1:71389/1‑143 (MQ=255)

                         aaGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGAt                                                                                                        >  1:396330/1‑143 (MQ=255)

                         aaGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGGCAGAt                                                                                                        >  1:459047/1‑143 (MQ=255)

                             tGGCAGTTCGTCACGTTAACGAGGGTGTAATTTCTAAGATCATCCCGATCGAAGATATGCCTTACTATGACAACGGTACGTCTGTAGACATCGTACTGTACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTc                                                                                                    <  2:452886/143‑1 (MQ=255)

                                      gtcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGCAGACATCGTACTGAACCAGCTGGGCGGACCGTCTCGTATGCACATCGGTCAGATCCCAGAAACCCAc                                                                                           >  2:41760/1‑143 (MQ=255)

                                       tcACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAACCGGTCCGCCCGTAGACATCGTACTGAACCAGCTAAGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCAcc                                                                                          >  1:48753/1‑143 (MQ=255)

                                        cACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCAcat                                                                                         >  1:456974/1‑141 (MQ=255)

                                         aCGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTg                                                                                        >  2:162243/1‑143 (MQ=255)

                                         aCGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTg                                                                                        <  2:190090/143‑1 (MQ=255)

                                                cAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCCCGAAACCCACCTGGGTATgg                                                                                 >  1:466507/1‑143 (MQ=255)

                                                     gtgtAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTAAAGTATGAACATCAGTCAGATACTCGAAAACAACATGGGTATGGCTGCg                                                                            >  1:40010/1‑143 (MQ=255)

                                                       gtAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGaa                                                                          >  2:236125/1‑143 (MQ=255)

                                                        tAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGACTCGAATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGaaa                                                                         >  1:254596/1‑143 (MQ=255)

                                                                      gccccGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACaa                                                           <  2:486119/141‑1 (MQ=255)

                                                                         ccGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTCAACCAACTAAACGTACAGTCACGAATGAACATCGGACAGATCCTCGAAAACCACATGGGTATGGCTGCGAAAAGTATCGGCGACAAGAt                                                        >  1:326222/1‑143 (MQ=255)

                                                                               gAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGATATAGCTGCGAAAGGTATCGGCGACACGATCAACGc                                                  >  1:92590/1‑143 (MQ=255)

                                                                               gAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCATCGAAAACAAACAGGGTATGGCTGCGAAAGGAATAGGCGACAAGATCAACGc                                                  >  1:95688/1‑143 (MQ=255)

                                                                                 ggagatGTCTTACGATCGAAACGGTACGCCGGTAGACATCGTACTGAACCAGCTGTGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCa                                                <  2:290565/139‑1 (MQ=255)

                                                                                 aGATCTGTCTTACGATGAAAGCGGTACGCCGGTAGGCATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCa                                                <  2:233085/143‑1 (MQ=255)

                                                                                   atgtgtcTTACGATGAAAACGGTACGCCGGTAGATATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATg                                              <  1:305941/137‑1 (MQ=255)

                                                                                         cTTACGATGAAAACGCGACGCCGGTAGACATCGTACTGAACCTGCTGGGTGTACTGTCTCGTATGAACATCGGTTAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGaaa                                        <  2:116223/143‑1 (MQ=255)

                                                                                           gaCGATGAAACCGGTACGCCTGTAGACATCGTACTGAATCAGCTGGGCGTACCGGCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGTCGACAAGATCAACGCCATGCTGAAAca                                      <  2:44008/142‑1 (MQ=255)

                                                                                                  aaaaCGGTACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGAATGGCTGAGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCaa                               >  1:431300/1‑143 (MQ=255)

                                                                                                        gtccGCCGGTAGACATCGTACCGTACCAGCAGGGCGTCCCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATCGCTGCGAAAGGTATCGGCGACAAGTTCAACGCCATGCTGAAACAGCAGCAAGAAGTc                         <  2:120870/140‑1 (MQ=255)

                                                                                                         tACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTTGTATGAACATCGGTCAGATCCTCGAAACCCACCGAGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTcg                        <  1:236125/143‑1 (MQ=255)

                                                                                                         tACGCCGGTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTcg                        <  2:342346/143‑1 (MQ=255)

                                                                                                           cGCCGGTAGACATCGTACTGAACCAGCTCACTGGGCGTTCTCGTATGAACATCGGTCAGATCCTCGAAACGCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTcgcg                      <  1:374064/143‑1 (MQ=255)

                                                                                                               ggTAGACATCGTACTGAACCAGCTGGGCGTCCGGTCTCGTATGTACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGCTTGGTATCGGCGACAAGATCAACGCAATGCTGAAATAGCAGCAAGAAGACGCGAAAc                  >  1:192354/1‑143 (MQ=255)

                                                                                                                gTAGACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGATAAAGAAGACAAGATCAACGCCATGCTAAAACAGCAGCAAGAAGACGCGAAACt                 >  1:185051/1‑143 (MQ=255)

                                                                                                                  aGACATCGTCCTGAACCAGCTGGCCGTCCCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTgc               <  2:396330/143‑1 (MQ=255)

                                                                                                                   gACATCGTGCTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGCAACCCACCGGGAGATGGCTGCGAAAGGTATCGGCGACCCGATCCACGCCCTGCTGATACAGCAGCACGAACTCTCGACACTgcg              >  1:83577/1‑143 (MQ=255)

                                                                                                                   gACATCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATGCTCGAAACCCACCTGGGTATGGCTGCGAGAGGTATCGGCGACACGATAAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGcaaacgcg              >  2:484966/1‑138 (MQ=255)

                                                                                                                     cATCGTACTGAACCAGCCGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGcgcg            <  2:40010/143‑1 (MQ=255)

                                                                                                                      aTCGTACTGAACCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCCCCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATAAACGCCATACAGAAAAAGCAACAAGAAGTCGCGACACTGCGCGa           >  1:429477/1‑143 (MQ=255)

                                                                                                                               aaCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCTACCTGGGTATGGCTGCCAACGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCACGAAGTAGCGAAACTGAGCGAATTCATACa  >  2:268137/1‑143 (MQ=255)

                                                                                                                               aaCCAGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCAGCGACAAGATCAAAGCCATGCTGAAAAAGCAGCAAGAAGTCGCGAAACTACGCGAATTCATcaa  >  1:222230/1‑141 (MQ=255)

TAAACGCCGTATCCAGCCTGGTGACAAGATGGCAGGTCGTCACGGTAACAAGGGTGTAATTTCTAAGATCAACCCGATCGAAGATATGCCTTACGATGAAAACGGTACGCCGGTAGACATCGTACTGAACCCGCTGGGCGTACCGTCTCGTATGAACATCGGTCAGATCCTCGAAACCCACCTGGGTATGGCTGCGAAAGGTATCGGCGACAAGATCAACGCCATGCTGAAACAGCAGCAAGAAGTCGCGAAACTGCGCGAATTCATCCA  >  NC_000913/4184412‑4184681

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