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
A21 F117 I1 R2	26	38.4	896262	90.9%	814702	136.0

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	CP000730	1,196,508	C→A	intergenic (+2563/‑1229)	ftsQ → / → ylmE	cell division protein FtsQ/hypothetical protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	CP000730	1,196,508	0	C	A	90.6%	78.9 / 1.8	33	intergenic (+2563/‑1229)	ftsQ/ylmE	cell division protein FtsQ/hypothetical protein
Reads supporting (aligned to +/- strand): ref base C (0/3); new base A (15/14); total (16/17)
Fisher's exact test for biased strand distribution p-value = 2.29e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.02e-01

ATTTTCGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGAAGAAAGACGT  >  CP000730/1196372‑1196647

aTTTTCGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGc                                                                                                                                         >  2:15763/1‑141 (MQ=255)

     cGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGc                                                                                                                                    >  1:183194/1‑141 (MQ=255)

         aCAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACt                                                                                                                                <  1:159989/141‑1 (MQ=255)

                        gAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCa                                                                                                                 >  2:54385/1‑141 (MQ=255)

                                aGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTc                                                                                                         <  1:215204/141‑1 (MQ=255)

                                          gttgtAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATtcatca                                                                                               <  1:15763/141‑1 (MQ=255)

                                            tgtAACAGTTATTGCAACCGGTTTTGATGACAAACCAACGGCACATGGTCGTCAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCaaa                                                                                             <  1:41183/141‑1 (MQ=255)

                                                    ttATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAg                                                                                     <  2:203684/141‑1 (MQ=255)

                                                                gTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAgtg                                                                         <  1:241081/141‑1 (MQ=255)

                                                                gTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAgtg                                                                         <  1:419005/141‑1 (MQ=255)

                                                                    tgatgaCAAACAAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACATCTAAAGATGAATCATTCACTTCAAAATCATCAAATGCACAAGCAACTGATAGTGTAAg                                                                     <  2:41840/141‑1 (MQ=255)

                                                                     gatgaCAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGt                                                                    <  2:346093/141‑1 (MQ=255)

                                                                                 aCATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACAt                                                        >  2:1757/1‑141 (MQ=255)

                                                                                 aCATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACAt                                                        >  2:117380/1‑141 (MQ=255)

                                                                                         tGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTaa                                                >  1:281171/1‑141 (MQ=255)

                                                                                            tCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATatctcgactac                                             >  2:340554/1‑131 (MQ=255)

                                                                                             cGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACatcaggttag                                            >  1:212406/1‑132 (MQ=255)

                                                                                               tAAATCTGGTAGCACTGGAGTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGAGGAAGCATTCACTTCAAACTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAagaaga                                          <  2:302090/141‑1 (MQ=255)

                                                                                                    cTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACTACTAAAGAAGATGata                                     >  2:222071/1‑141 (MQ=255)

                                                                                                    cTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGata                                     >  1:109628/1‑141 (MQ=255)

                                                                                                     tGGTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGatat                                    <  1:4398/141‑1 (MQ=255)

                                                                                                      ggTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATAtt                                   >  2:356213/1‑141 (MQ=255)

                                                                                                       gTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGa                                                                                                                        <  2:181333/55‑1 (MQ=255)

                                                                                                       gTAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGa                                                                                                                        >  1:181333/1‑55 (MQ=255)

                                                                                                        tAGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTcc                                 <  1:50279/141‑1 (MQ=255)

                                                                                                         aGCACTGGATTCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCt                                <  2:175084/141‑1 (MQ=255)

                                                                                                         aGCACTGGATTCGGAACAAGCCGAAATACTTGGATCAACGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAACTGCACAAGCAACTGTTAGTGTAATTGAAAGAACACATACAACTAAAGAAAAGGATATTCCt                                >  2:145394/1‑141 (MQ=255)

                                                                                                                   tCGGAACAAGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTa                      >  2:56493/1‑141 (MQ=255)

                                                                                                                           aGCGTAAATACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGAAACTGATAGTGTAAGTGAAAGAACAAATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATaga              >  2:167423/1‑141 (MQ=255)

                                                                                                                           aGCGTAAATACTGATAGCAATGCAACTTCGAAAGATGAATCATGCACGTCTAATTCAGCAAATGCACAAGCAACTGATAGTGGAAGTGAAAGAACACATACAACCAAAGAAGATGATATTCACAGCTTCATTAGAAATaga              >  2:84883/1‑141 (MQ=255)

                                                                                                                                aaaTACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGagaaga         <  2:82320/141‑1 (MQ=255)

                                                                                                                                  aTACTTATAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGaagaaa       <  2:254003/141‑1 (MQ=255)

                                                                                                                                       tCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGAAGAAAGACGt  <  2:361273/141‑1 (MQ=255)

ATTTTCGGTACAGTTATTAATCCTGAATTACAAGATGAGATTGTTGTAACAGTTATTGCAACTGGTTTTGATGACAAACCAACATCACATGGTCGTAAATCTGGTAGCACTGGATTCGGAACAAGCGTAAATACTTCTAGCAATGCAACTTCTAAAGATGAATCATTCACTTCAAATTCATCAAATGCACAAGCAACTGATAGTGTAAGTGAAAGAACACATACAACTAAAGAAGATGATATTCCTAGCTTCATTAGAAATAGAGAAGAAAGACGT  >  CP000730/1196372‑1196647

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 12 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 37 ≤` `ATCG/ATCG` `< 41 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A