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 F56 I0 R1	218	83.1	3292392	95.3%	3137649	126.7

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	CP006881	1,672,787	G→T	26.0%	M1M (ATG→ATT) †	U712_08615 →	Flagellar biosynthesis protein flhF

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP006881	1,672,787	0	G	T	26.0%	42.3 / 2.7	39	M1M (ATG→ATT) †	U712_08615	Flagellar biosynthesis protein flhF
Reads supporting (aligned to +/- strand): ref base G (14/13); new base T (9/2); total (23/16)
Fisher's exact test for biased strand distribution p-value = 1.45e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

TGTGAAGCAGCTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGTCATATTAAATTCGAAAAAAATTAAAAAGCGAAAATGGTTTGGCCTCGTCAACAAGCCTG  >  CP006881/1672680‑1672923

tgtgAAGCAGCTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTTCAATg                                                                                                            >  7:9678/1‑138 (MQ=255)

    aaGCAGCTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGCTATTTAAAGATAATAAAAAAATATAATGCTGCTTCAATGCaag                                                                                                        >  5:204523/1‑138 (MQ=255)

      gcagcTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATTAAAATAAAAAAATTTACTTCTGCTTAAATTCaagaag                                                                                                     >  8:139411/1‑139 (MQ=255)

        agcTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTTATTAAAAAAAAAAAAATTAATTCTGCTTCAATGGAAGAAGCg                                                                                                   >  3:43865/1‑139 (MQ=255)

                gAACTGTACTTCCATGCTCTTGCGGTAATCTCTTATAACGAACTTGAGGCGAATGTTTAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTGCAATGCAAGAAGCGGCACTtct                                                                                           <  5:51320/139‑1 (MQ=255)

                gAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACtt                                                                                             <  5:149434/137‑1 (MQ=255)

                        cTTCCCTGATCTTCCGGTCATCTCTTATACCGAACTTGAGGCTAATGTTGAGGTACAAAGCATTGGAGTTGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGaa                                                                                   <  3:222754/139‑1 (MQ=255)

                        cTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGaa                                                                                   <  7:139965/139‑1 (MQ=255)

                           cccTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATTAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGaa                                                                                   >  4:144340/1‑136 (MQ=255)

                             cTGATGTTCCGGTACTCTCTAATAAAGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAagag                                                                              <  7:144545/139‑1 (MQ=255)

                             atGATCTTCCGGTCCTCTCTTATAACGAACTTGAGGCGAATGTTGTGGTACAATGCATTGGAGTGGTGTATATTTAATCAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAagag                                                                              <  2:169772/138‑1 (MQ=255)

                                ttCTTCCGGTACGATCTTATAACGAACTTGAGGCGAATGTTTAGGTACAAAGCTTTGGAGTGGTGTATATTTAATTAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGtt                                                                            <  8:66935/137‑1 (MQ=255)

                                ctcatCCGGTACTCACTTAAACCGAAATTCAGGCGAATGTTTAGGTACAAAGATTTGGATTGGTGTATATTTAATGAAAATAAAAAAATTTACTGCTGCTTAAATGAAAGAAGCGGCACTTCTCATCAGAAAAGAGTTa                                                                           <  1:154488/135‑1 (MQ=255)

                                atgttCCGTTACTCTCTTATAACTAACTTTAGGCGAATTATGAGGTACAAAGCTTTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGtt                                                                            <  5:264989/135‑1 (MQ=255)

                                aTCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGTTATTTAATTAAAAAAAAAAAAATTAATGCTGCATAAATTCAAAAAGCGGCACATAGCATCAGAAAAAATTTa                                                                           >  1:385505/1‑139 (MQ=255)

                                aTCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTTATTAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACGTCTCATAAGAAAAAAGTTa                                                                           >  5:383704/1‑139 (MQ=255)

                                aTCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTTATGAAAATAAAAAAATTTACTGGTGCTTCAATGCAAGAAGCGGCACGTCTCATCAGAAAAGAGTTa                                                                           >  5:101161/1‑139 (MQ=255)

                                aTCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTAATGCTGCTTCAATGCAAGAAGCGGCACTTCTAATCAGAAAAGAGt                                                                             >  3:155715/1‑137 (MQ=255)

                                aTCTTCCGGTACTCTCTTATAACCAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGtt                                                                            <  8:9678/138‑1 (MQ=255)

                                aTCTACCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGCACAAAGCCTTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGtt                                                                            <  6:101773/138‑1 (MQ=255)

                                   ttCCGGTACTCTCTTATAACGAACTAGAGGCGAATGTTGAGGTACAAAGCAGTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTTCTTCAATGCAAGAAGCGGCACTTGTAATCAGAAAAGAGTTAgg                                                                         >  7:66935/1‑138 (MQ=255)

                                              tctTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGAATTGGAGTGGTGGATATTTAATTAAAAAAAAAAAATTTACTTCTGCTTAAATGCAATAATCGGCACATCTCATCAGAAAATAGTTATGTAATGCAGCGGt                                                             >  6:154846/1‑139 (MQ=255)

                                                ttATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGt                                                             <  3:144340/137‑1 (MQ=255)

                                                   taACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGTGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGaa                                                                                   <  2:35778/112‑1 (MQ=255)

                                                   taACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGaa                                                                                   >  1:35778/1‑112 (MQ=255)

                                                        aaCTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTTATTAAAATAAAAAAATTTAATGCTGCTTCAATGCAAGAAGCGGCACTTGTCATCAGAAAAGAGTTAGGTAATGAAGCGGGGATATTAAAt                                                   >  1:358889/1‑139 (MQ=255)

                                                        aaCTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGTCATATTAAAt                                                   >  5:147727/1‑139 (MQ=255)

                                                          cTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGTAATTTAATGAAAAAAAAAAAAATTACTGCTGCGTCAATTCAACAAGCGGCACTTCTCATAAGATAACAGTTAGGAAATGAAGCGGTCATATTAAAtta                                                 >  7:44666/1‑138 (MQ=255)

                                                          cTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGGTATTTAATTAAAATAAAAAAATTTAATGCTGCTTCAATGGAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGGGATATTTAATTc                                                 >  5:267629/1‑139 (MQ=255)

                                                          cTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATTAAAATAAAAAAATTTAATGCAGCTTCAATTCAAGAATCGGCACATATCATAAAAAAATAGTTATGTAATTAAACGGTCATATAAAAtta                                                 >  3:97043/1‑138 (MQ=255)

                                                                   aaTGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGTCATATTAAATTCGAAAAAAAt                                        >  8:90311/1‑139 (MQ=255)

                                                                               cAAAGCATTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGTCATATTAAATTCGAAAAAAATTAAAAAGCGaaa                            <  7:139411/139‑1 (MQ=255)

                                                                                 aaGCATTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTTCAATGCAATAAGCGGCACTTCTCATCAGAAAATAGTTAGGTAATGAAGCGGTCATATTAAATTCGAAAAAAATTAAAAAGCGAAAAt                          >  5:150631/1‑139 (MQ=255)

                                                                                      ttGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTAATGCTTCTTCAATTCAATAAGCGGCACATATCATCAGAAAAAATTTAGCTAAAGAAACAGTTATATTAAATTCTAAAAAAATTAAAAATCGAAAATAGttt                     >  8:250753/1‑139 (MQ=255)

                                                                                       tGGAGTGGTGGATTTTTTATGAAAATAAAAAAATTTAATGCTGGATCAATGCAAGAAGCGGCACTTGTCATCAGAAAAGAGTTAGGTTAATAAGCGGTCATATTTAATTCGAAAAAAATTTAAAAGCGTAAATTGTTTg                    >  6:99170/1‑139 (MQ=255)

                                                                                       tGGAGTGGTGGATATTTTATGAAAATAAAAAAATTTACTGCTGCGTCAATGCAAGAAGCGGGACTTCTGATCAGAAAAGGGTTAGGTAATTCAGCGGTCAGAATAAATTCGAAAAAAATTAAAAAGCGCAAATGGTTTg                    >  4:195738/1‑139 (MQ=255)

                                                                                                        aattaaaattaaAAAATTTACTTGTGCTTCAATGCATGAAGCGGCACTTTTCATCAGAAAAGAGTTAGTTAATGAAGCGGTCATATTAAATTCTAAAAAAATTAAAAAGCGAAAATTGTTTGGCCTCGTCAACAAGcc    <  8:44666/138‑1 (MQ=255)

                                                                                                        aaTTAAAATAAAAAAATTTCCTGCTGCTCCAATGCAAGACGCGGCACTTCTCATCAGAAAACAGTTACGTAATGAAGCGGTCATATTAAATTCGAAAAAAATTAAAAAGCGAAAATGGTTTGGCCTCGTCAACAAGcc    <  6:302978/138‑1 (MQ=255)

                                                                                                        aaTGAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGTCATATTAAATTCGTTAAAAATTAAAAAGCGAAAATGGTTTGGCCTCGTCAACAAGCct   >  2:8215/1‑139 (MQ=255)

                                                                                                         aTGAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGAACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGTCATATTAAATTCGAAAAAAATTAAAAAGCGAAAATGGTTTGGCCTCGTCAACAAGCctg  <  6:150631/139‑1 (MQ=255)

TGTGAAGCAGCTACTGGAACGGTACTTCCCTGATCTTCCGGTACTCTCTTATAACGAACTTGAGGCGAATGTTGAGGTACAAAGCATTGGAGTGGTGGATATTTAATGAAAATAAAAAAATTTACTGCTGCTTCAATGCAAGAAGCGGCACTTCTCATCAGAAAAGAGTTAGGTAATGAAGCGGTCATATTAAATTCGAAAAAAATTAAAAAGCGAAAATGGTTTGGCCTCGTCAACAAGCCTG  >  CP006881/1672680‑1672923

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 15 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A