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
A1 F104 I0 R1	106	58.2	1336546	90.2%	1205564	141.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP000730	1,440,085	G→T	100%	intergenic (‑45/‑891)	cspA ← / → xpaC	cold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,440,085	0	G	T	100.0%	131.7 / NA	47	intergenic (‑45/‑891)	cspA/xpaC	cold shock protein CspA/5‑bromo‑4‑chloroindolyl phosphate hydrolysis protein XpaC
Reads supporting (aligned to +/- strand): ref base G (0/0); new base T (14/33); total (14/33)
Rejected as polymorphism: Frequency below/above cutoff threshold.
Rejected as polymorphism: Variant not supported by required number of reads on each strand.

TGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTAT  >  CP000730/1439948‑1440222

tGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCat                                                                                                                                        >  2:182656/1‑141 (MQ=255)

tGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCat                                                                                                                                        >  2:538693/1‑141 (MQ=255)

tGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCat                                                                                                                                        >  2:451957/1‑141 (MQ=255)

 gAAAAATGTACGAATACGTCCTTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCata                                                                                                                                       <  2:622128/141‑1 (MQ=255)

 gAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCata                                                                                                                                       <  1:409457/141‑1 (MQ=255)

     aaTGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTAc                                                                                                                                   <  1:203572/141‑1 (MQ=255)

                     aTTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCaaa                                                                                                                   >  1:237125/1‑141 (MQ=255)

                      ttttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGTAAAt                                                                                                                  >  1:391927/1‑141 (MQ=255)

                      ttttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAAt                                                                                                                  >  1:96067/1‑141 (MQ=255)

                      ttttCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAAt                                                                                                                  >  1:391216/1‑141 (MQ=255)

                       tttCTCCTTCAACTTCGGTAAAGTCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACACAAAATACATGCAAAtt                                                                                                                 <  1:331437/141‑1 (MQ=255)

                           tcCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTCCAAAAAATACATGCAAATTTCAc                                                                                                             >  1:351704/1‑141 (MQ=255)

                               tCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAATATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCaa                                                                                                         <  1:141350/141‑1 (MQ=255)

                               tCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCATTCaa                                                                                                         <  1:453186/141‑1 (MQ=255)

                               tCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCaa                                                                                                         <  1:93226/141‑1 (MQ=255)

                                cAACTTCGATAAACCCGAATCCTTTTTCACCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCaaa                                                                                                        <  2:312697/141‑1 (MQ=255)

                                      cGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCt                                                                                                  <  1:86315/141‑1 (MQ=255)

                                             accGAATTCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACAAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAat                                                                                           <  2:323263/140‑1 (MQ=255)

                                                 aaaccTTTTTCCGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCCCCAAGACTACCATTCAATCAATATGCTTAATCTCATATTATAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATgg                                                                                       <  1:294912/138‑1 (MQ=255)

                                                  tgccTTTTTCAGCCTTAAACCATTTATCTGTATCTTGATTGATAATCTGAATCATAAAAGAATAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAGTTTCACTTAAATAATCTCTGCAATATGGa                                                                                      <  2:208656/139‑1 (MQ=255)

                                                   accTTTTTCACCGTTAAACCATTTAACTGTACCTTGTTTCATATTCTGAAACCTCCAATACTAAAATTCATTCAATTTGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGaa                                                                                     <  2:229222/140‑1 (MQ=255)

                                                          tCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGATTAatcat                                                                              <  2:243295/141‑1 (MQ=255)

                                                          tCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatcat                                                                              <  2:318006/141‑1 (MQ=255)

                                                          tCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATGCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAatcat                                                                              <  2:476851/141‑1 (MQ=255)

                                                            aGCGTTAGACCAATTAGCTGTACCTTGTTTCATAATCTGAAACCTCCAAGGCTAAAATTCATTCAATATGCTTATTCTCATATTACCAAAAATACATGCTAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCt                                                                            <  2:598799/141‑1 (MQ=255)

                                                             gCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTg                                                                           <  1:445646/141‑1 (MQ=255)

                                                             gCGTTAAACCATTTAACTGTACCTTGTTTCAGAATCTGAAACCTCCAACACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTg                                                                           <  1:76019/141‑1 (MQ=255)

                                                              tgTTAAACTATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTTCAATATGGAATAATAATCttc                                                                          >  2:517830/2‑139 (MQ=255)

                                                                      cATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTg                                                                  <  1:288227/141‑1 (MQ=255)

                                                                      cATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTg                                                                  <  1:536514/141‑1 (MQ=255)

                                                                             ttGTCCCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAACATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATtata                                                           <  1:521928/140‑1 (MQ=255)

                                                                                tACCTTGTGGCATAATCTGAAACCTCCAAGACTAAAATTCATGCAATATGCTTATTCTCATATTACAAAAAATACAGGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTg                                                        <  2:151352/141‑1 (MQ=255)

                                                                                 cccTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGc                                                       <  1:175586/140‑1 (MQ=255)

                                                                                         tCATAATCTGAAACCACCAAGACTAAAACTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGttatta                                               <  2:354196/141‑1 (MQ=255)

                                                                                                 tGAAACCTCCGATACGAAAATTCATTGAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAAttt                                       >  2:558071/1‑140 (MQ=255)

                                                                                                     aCCTCCAAGACTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGcaat                                   >  1:648760/1‑141 (MQ=255)

                                                                                                             aaCTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACaataat                           <  1:643059/140‑1 (MQ=255)

                                                                                                              aCTAAAATTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAataata                          <  1:111859/141‑1 (MQ=255)

                                                                                                                 aaaaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaa                       >  2:35984/1‑141 (MQ=255)

                                                                                                                 aaaaTTCATTCAATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaa                       >  2:545293/1‑141 (MQ=255)

                                                                                                                  acattcattcAATATCCTTATTCTCATATTACAAAAAATACATGCAAATTTCTCTCTATTATTCTTTGTAATATGGAATAATCATCTGATTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATaaaaa                      <  2:55626/139‑1 (MQ=255)

                                                                                                                      tctgtcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAatat                  <  2:411447/137‑1 (MQ=255)

                                                                                                                      tcattcaATATGCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACATTAATAAAAAatat                  >  1:46372/1‑141 (MQ=255)

                                                                                                                                ttcTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATc        <  2:337735/139‑1 (MQ=255)

                                                                                                                                 gCTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCa       <  2:551231/141‑1 (MQ=255)

                                                                                                                                  cTTATTCTCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCaa      <  2:515660/141‑1 (MQ=255)

                                                                                                                                      ttCTCATATTACAAAAAAGACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAattat  <  2:33555/141‑1 (MQ=255)

TGAAAAATGTACGAATACGTCATTTTCTCCTTCAACTTCGATAAAGCCGAATCCTTTTTCAGCGTTAAACCATTTAACTGTACCTTGTTTCATAATCTGAAACCTCCAAGACTAAAATTCATTCAATATGCTTATTCGCATATTACAAAAAATACATGCAAATTTCACTCAAATATTCTTTGCAATATGGAATAATCATCTGCTTAACTTGTATTATAGTGCAGTTATTACCAAATTGCAATACAATAATAAAAAATATTCATTTAATCAATTAT  >  CP000730/1439948‑1440222

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 13 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A