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
A5 F109 I1 R1	27	23.1	511165	92.8%	474361	140.9

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	2,236,856	A→T	L308I (TTA→ATA)	rho ←	transcription termination factor Rho

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	2,236,856	0	A	T	97.0%	99.6 / ‑4.8	33	L308I (TTA→ATA)	rho	transcription termination factor Rho
Reads supporting (aligned to +/- strand): ref base A (1/0); new base T (16/16); total (17/16)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.70e-01

TGTTCCTTTAAATTCTTCGTAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTAAAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTAAAATAATGACATCTTCCCCAATTTCTACTAAACGCTTTGCACG  >  CP000730/2236722‑2236991

tGTTCCTTTAAATTCTTCGTAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGagga                                                                                                                                   >  2:214691/1‑138 (MQ=255)

tGTTCCTTTAAATTCTTCGTAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGc                                                                                                                                   >  2:423992/1‑141 (MQ=255)

      tgtAAATTCTTCGTGTATCCTATCGTCCTTACGTGAACCCGTATCAACTAGTGCAGTTGCAAGTATTGTTAAACTTCTACCCGCTTCTATACTTCTCGCTGCACCGAAGATTGTTTGTGTTTTGTGTATAGATGCAGGATc                                                                                                                             <  2:339770/139‑1 (MQ=255)

       ttAAATTCTTCGTAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCt                                                                                                                            <  2:360271/141‑1 (MQ=255)

         aaaTTCTTCGTAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTaa                                                                                                                          <  2:82959/141‑1 (MQ=255)

          aatctctcGTAAACCATTCTGTCCATACCTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTaaa                                                                                                                         <  2:95159/135‑1 (MQ=255)

          aaTTCTTCGTAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATACTTTTGGTTTGTGTATAGATGCAGGATCTaaa                                                                                                                         <  2:377813/141‑1 (MQ=255)

          aaTTCTTCGGAAATCATATCGTCGATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTTCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTaaa                                                                                                                         <  2:60051/141‑1 (MQ=255)

          aaTTCTTCCTAAATCATATCGTCCCTACGTGAACCCGTATCAACGAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTaaa                                                                                                                         <  2:965/141‑1 (MQ=255)

                tcGTAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCt                                                                                                                   <  2:167548/141‑1 (MQ=255)

                   tAAATCATATCGTCCATACGTGAACCCCTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAAGATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGAt                                                                                                                <  2:406923/141‑1 (MQ=255)

                            tCGTCAATACGTGAACCCGTATCAGCTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGTTAATGTCCGa                                                                                                       >  2:167783/1‑141 (MQ=255)

                                 cATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTGTAGATGCAGGATCTAAACCACCTGATAATGTACGACCACt                                                                                                  >  2:342365/1‑141 (MQ=255)

                                    cagggAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTtgg                                                                                               <  2:250608/137‑1 (MQ=255)

                                       tGAACCCGTATCAATTAATGCATTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCTCCTGATAATGTACGACCACTtggtgg                                                                                            <  2:308281/141‑1 (MQ=255)

                                          aCCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAAt                                                                                         <  2:55289/141‑1 (MQ=255)

                                           cccGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATa                                                                                        <  2:339963/141‑1 (MQ=255)

                                           cccGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATa                                                                                        >  2:251127/1‑141 (MQ=255)

                                              gTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACt                                                                                     >  2:158141/1‑141 (MQ=255)

                                               tATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTa                                                                                    >  2:472373/1‑141 (MQ=255)

                                                 tCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAg                                                                                  >  2:128957/1‑141 (MQ=255)

                                                        atccAGTGGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAg                                                                           <  2:473931/138‑1 (MQ=255)

                                                               tGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGc                                                                    <  2:193201/141‑1 (MQ=255)

                                                                   aGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGCATGCTTTTGGTTTCTGTATAACTGCAGGATCTAAACCACCTGATAATGTACGACACATTGGTGGAATCACTAACTTATAAGCCCGTGCTAAt                                                                >  2:469792/1‑141 (MQ=255)

                                                                     tATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCAGACAACAATAACAACAATTGGTGTATATATGGAAGACGAAGATAACCGAAAAATGATCTACTACGTGGTGGAATAACTAAGTGATAAGCGCGTGCTaccct                                                              >  2:477815/1‑137 (MQ=255)

                                                                                     cccGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTAAAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCAtt                                              >  1:6616/1‑141 (MQ=255)

                                                                                       cGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCAttga                                            >  2:48526/1‑139 (MQ=255)

                                                                                       cGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTaa                                            >  2:175972/1‑141 (MQ=255)

                                                                                       cGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTaa                                            >  2:164078/1‑141 (MQ=255)

                                                                                             aaTATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTACaataat                                      >  2:482228/1‑141 (MQ=255)

                                                                                                         tGCACCGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTAAAATAATGACATCTTcccc                          <  2:388942/141‑1 (MQ=255)

                                                                                                             ccGAAGAATGCTTTTGGTTTGTGTATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTGATAAGCGCGTGCTAATCTCGTTATAGAATCCATTAAAATAATGACATCTTCCCCAAtt                      >  2:327287/1‑141 (MQ=255)

                                                                                                                                 gtgtATAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTAAAATAATGACATCTTCCCCAATTTCTCCTAAACGCTTTGCACg  >  2:378162/1‑141 (MQ=255)

TGTTCCTTTAAATTCTTCGTAAATCATATCGTCCATACGTGAACCCGTATCAACTAATGCAGTTGCAAGTATTGTTAAACTTCCACCCGCTTCAATATTTCTCGCTGCACCGAAGAATGCTTTTGGTTTGTGTAAAGATGCAGGATCTAAACCACCTGATAATGTACGACCACTTGGTGGAATAACTAAGTTATAAGCGCGTGCTAATCTCGTTATAGAATCCATTAAAATAATGACATCTTCCCCAATTTCTACTAAACGCTTTGCACG  >  CP000730/2236722‑2236991

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