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
A17 F104 I0 R1	40	45.6	1767846	90.1%	1592829	142.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	NC_000913	4,196,196	T→C	100%	intergenic (‑97/+136)	thiC ← / ← rsd	phosphomethylpyrimidine synthase/regulator of sigma D

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	4,196,196	0	T	C	100.0%	143.7 / NA	46	intergenic (‑97/+136)	thiC/rsd	phosphomethylpyrimidine synthase/regulator of sigma D
Reads supporting (aligned to +/- strand): ref base T (0/0); new base C (17/29); total (17/29)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

CGCGTTGTTCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCA  >  NC_000913/4196063‑4196334

cgcgTTGTTCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGc                                                                                                                                   <  2:756905/143‑1 (MQ=255)

  cgTTGTTCGCGGCGGGTCAGTTTCGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAg                                                                                                                                 <  1:464308/143‑1 (MQ=255)

  cgTTGTTCGCGGCGGGGCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAg                                                                                                                                 <  2:178729/143‑1 (MQ=255)

     tgttCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGACGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCGTGCTCCCTTCGCAGGTa                                                                                                                              <  2:20627/143‑1 (MQ=255)

      gtccgcgGCGGGTCAGTGTTGCGCCTGGCATAGCTCATGCCGAAAAGTGAGGGCCGGGGCTCGCCAGACGACGGCTGAAGCAAGAGCCGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCCCCCTTCGCAGGTAt                                                                                                                             <  2:820746/140‑1 (MQ=255)

        tCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTTCTTCCTTCGCCGGTATTa                                                                                                                           >  1:649490/1‑143 (MQ=255)

           cggcggGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCCAGAGACGATCGCCGCAGGGGCGATGCCATAGCAGATTAACTCTTTCTCCCTTCGCAGGTCTTAGcc                                                                                                                        >  2:690273/1‑143 (MQ=255)

           cggcggGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTCTGAGcc                                                                                                                        >  2:48117/1‑143 (MQ=255)

             gcggGTCAGTTGTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCACACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTg                                                                                                                      <  2:435781/143‑1 (MQ=255)

                     gTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACCCTTGCTCCCTTCGCCGCTATCAGCCTGATCAGGtt                                                                                                              >  2:654591/1‑143 (MQ=255)

                      ttttGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATGAACTCTTGCTCCCTTCGCAGGTATTAGCGGGATCAggggc                                                                                                             >  1:24589/1‑140 (MQ=255)

                         tgttgCTGACTCACCTCATCCCAATCACTTGCGGACTGGGCTTGTTAGACGACTGATGCAGCAAGACACGTTTGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCTTTCGCAGGTATTAGCCTGATCAGGTTCcgc                                                                                                          <  2:414300/143‑1 (MQ=255)

                          gttgCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAGCTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCcgcg                                                                                                         <  2:793842/143‑1 (MQ=255)

                          gttgCAGACAGAGCTCGTTCCAGAAAGTTAAGGACTTGGCGTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCcgcg                                                                                                         <  2:364929/143‑1 (MQ=255)

                           ttgCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCgg                                                                                                        >  1:346156/1‑143 (MQ=255)

                             gCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCCGac                                                                                                      >  2:202522/1‑142 (MQ=255)

                              cAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGTAATTTATACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATc                                                                                                     <  2:181543/143‑1 (MQ=255)

                                 aCATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCg                                                                                                  <  2:293245/143‑1 (MQ=255)

                                   agaGCTCATTCAGAGAGGTTAAGGGCGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCAGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGaa                                                                                                <  2:313911/141‑1 (MQ=255)

                                   aTAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGaa                                                                                                <  1:275021/143‑1 (MQ=255)

                                        tCATTCCAAAAAGTTAAGGACGTGGCGTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAAc                                                                                           <  2:730417/143‑1 (MQ=255)

                                         cATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACg                                                                                          <  2:855796/143‑1 (MQ=255)

                                               aaaaaGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGGCTCa                                                                                    >  2:737989/1‑143 (MQ=255)

                                                   aGTTAAGCACGTGGCCTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCa                                                                                <  1:47595/143‑1 (MQ=255)

                                                        aGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTaa                                                                           <  1:524409/143‑1 (MQ=255)

                                                        aGGACGGGGCTTTCCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTaa                                                                           <  1:538678/143‑1 (MQ=255)

                                                          gACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGGGCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAgg                                                                         >  1:373745/1‑143 (MQ=255)

                                                          gACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAgg                                                                         <  1:791700/143‑1 (MQ=255)

                                                                     gtagagGACGGATGAAGCAAGAGACGGTCGCTGCAGGGGCGAGGCGATAGCAGATGAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCACGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACaa                                                              <  2:554864/141‑1 (MQ=255)

                                                                        gacgacGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGaa                                                           <  1:801118/143‑1 (MQ=255)

                                                                         acgacgGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGAACTCCGTCAAGaaa                                                          <  2:357562/143‑1 (MQ=255)

                                                                                aTGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATCAACGGTCTCAGCCAGTTAAGGCACTCCGACAATAAATTAGccc                                                   >  1:16451/1‑143 (MQ=255)

                                                                                        agagACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATg                                           >  2:690950/1‑143 (MQ=255)

                                                                                         gagaCGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGCTCAGGTTCCGCAGATCCCGACTAAACGGGCTCAGCCACGTCAGGCACCCCGCCAACACATTAGCCCAGCACATgg                                          >  1:732389/1‑143 (MQ=255)

                                                                                         gagaCGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTACCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATgg                                          >  1:461963/1‑143 (MQ=255)

                                                                                          agaCGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCGGCCCGTTAAGGCACTCCGGCAAGAAATTAGCCCCGCAAATggg                                         >  2:359652/1‑143 (MQ=255)

                                                                                                         gggCGATGCGATAGCAGATTAACTCTTGCTCCCTTCGCAGGTAGTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAAGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCACTGAATCTAAAt                          >  2:687318/1‑143 (MQ=255)

                                                                                                           gcgatgcgatAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTa                        <  1:721739/143‑1 (MQ=255)

                                                                                                             gatgcgatAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGCAAATTAcg                      >  2:866307/1‑143 (MQ=255)

                                                                                                              atgcgttACCAGATTAACTCTTGCTCTCTTCGCAGGTATTAGCGTGATTAGGTTCCGCGGCTCCCGAGTAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTAcgc                     <  2:660768/143‑1 (MQ=255)

                                                                                                                 cgatAGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGtt                  <  2:778377/143‑1 (MQ=255)

                                                                                                                     aGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACa              <  1:705063/143‑1 (MQ=255)

                                                                                                                     aGCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACa              <  1:813213/143‑1 (MQ=255)

                                                                                                                      gCAGATTAACTCTTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGCAAATTACGCGTTAACAg             <  1:866307/143‑1 (MQ=255)

                                                                                                                                tctTGCTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTc   >  1:723776/1‑143 (MQ=255)

                                                                                                                                 ctTGCTCCTTTCGCAGGTAGTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACGCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCa  <  2:30785/143‑1 (MQ=255)

CGCGTTGTTCGCGGCGGGTCAGTTTTGTTGCAGACATAGCTCATTCCAAAAAGTTAAGGACGTGGCTTGTCAGACGACGGATGAAGCAAGAGACGATCGCCGCAGGGGCGATGCGATAGCAGATTAACTCTTGTTCCCTTCGCAGGTATTAGCCTGATCAGGTTCCGCGGATCCCGAATAAACGGTCTCAGCCAGTTAAGGCACTCCGACAAGAAATTAGCCCCGCAAATGGGGCATTGAATGTAAATTACGCGTTAACAGCGCAGAACTCA  >  NC_000913/4196063‑4196334

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 8 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A