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 F1 I1 R1	64	69.7	3300380	93.4%	3082554	111.2

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	annotation	gene	description
RA	NC_000913	3,830,989	T→C	V178A (GTT→GCT)	yicH →	putative inner membrane‑anchored periplasmic AsmA family protein

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	NC_000913	3,830,989	0	T	C	88.0%	139.4 / 8.6	50	V178A (GTT→GCT)	yicH	putative inner membrane‑anchored periplasmic AsmA family protein
Reads supporting (aligned to +/- strand): ref base T (3/3); new base C (20/24); total (23/27)
Fisher's exact test for biased strand distribution p-value = 1.00e+00
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 3.43e-01

GCCCGAATAGCGAATGGAAACTGAGCGCGCAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGTTCCTGCCACCAATGTACTGATTGAAGGCAGTATTGATAACGATCGCGTTACGCTGACTAACCTGGGTGCCGACATCGCCCGCGGGACATTAACCGGAAACGCGCAGCGTAACGCCGACGGCAGCTGGC  >  NC_000913/3830854‑3831117

gCCCGAATAGCGAATGGAAACTGAGCGCGCAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTcc                                                                                                                               >  2:746162/1‑139 (MQ=255)

 cccGAATAGCGAATGGAAACTGAGCGCGCAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCt                                                                                                                              <  1:1255401/139‑1 (MQ=255)

 cccGAATAGCGAATGGAAACTGAGCGCGCAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCt                                                                                                                              >  1:893063/1‑139 (MQ=255)

   cGAATAGCGAATGGAAACTGAGCGCGCAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGc                                                                                                                            <  2:168059/139‑1 (MQ=255)

      aTAGCGAATGGAAACTGAGCGCGCAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGccac                                                                                                                         <  2:1296355/139‑1 (MQ=255)

        aGCGAATGGAAACTGAGCGCGCAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGccacca                                                                                                                       <  2:368490/139‑1 (MQ=255)

             aTGGAAACTGAGCGCGCAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTa                                                                                                                  <  1:742874/139‑1 (MQ=255)

               ggAAACTGAGCGCGCAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGAACt                                                                                                                >  2:864739/1‑139 (MQ=255)

                   aCTGAGCGCGCAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGAtt                                                                                                            <  2:966142/139‑1 (MQ=255)

                       aGCGCGCAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAg                                                                                                        <  1:1544417/139‑1 (MQ=255)

                       aGCGCGCAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAg                                                                                                        >  1:395779/1‑139 (MQ=255)

                       aGCGCGCAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAg                                                                                                        >  1:123269/1‑139 (MQ=255)

                       aGCGCGCAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGT‑AAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAgg                                                                                                       >  1:871927/1‑139 (MQ=255)

                        gcgcgcAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAgg                                                                                                       <  2:864183/139‑1 (MQ=255)

                          gcgcAGCGGGTAAATGGCGGTGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCa                                                                                                     <  1:1611529/139‑1 (MQ=255)

                           cgcAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAg                                                                                                    >  2:1472070/1‑139 (MQ=255)

                           cgcAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAg                                                                                                    <  2:280740/139‑1 (MQ=255)

                             cAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAGTa                                                                                                  <  2:123269/139‑1 (MQ=255)

                             cAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAGTa                                                                                                  <  1:1271816/139‑1 (MQ=255)

                             cAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGAACTGATTGAAGGCAGTa                                                                                                  <  1:864739/139‑1 (MQ=255)

                              aGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAGTAt                                                                                                 >  2:484939/1‑139 (MQ=255)

                                             gcgTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGc                                                                                                                            >  1:404961/1‑97 (MQ=255)

                                             gcgTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGc                                                                                                                            <  2:404961/97‑1 (MQ=255)

                                             gcgTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAGTATTGATAACGATCGCGt                                                                                  >  1:1330322/1‑139 (MQ=255)

                                                           tCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAGTATTGATAACGATCGCGTTACGCTGACTAAcc                                                                    <  1:784082/139‑1 (MQ=255)

                                                             aCCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGTTCCTGCCACCAATGTAc                                                                                                                 <  1:1623455/92‑1 (MQ=255)

                                                             aCCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGTTCCTGCCACCAATGTAc                                                                                                                 >  2:1623455/1‑92 (MQ=255)

                                                                                   ggTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAGTATTGATAACGATCGCGTTACGCTGACTAACCTGGGTGCCGACATCGCCCGCGGGa                                            >  2:857283/1‑139 (MQ=255)

                                                                                     tACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAGTATTGATAACGATCGCGTTACGCTGACTAACCTGGGTGCCGACATCGCCCGCGGGACa                                          <  1:1472070/139‑1 (MQ=255)

                                                                                       cGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAGTATTGATAACGATCGCGTTACGCTGACTAACCTGGGTGCCGACATCGCCCGCGGGACAtt                                        >  1:222633/1‑139 (MQ=255)

                                                                                        gAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAg                                                                                                    >  1:1621767/1‑78 (MQ=255)

                                                                                        gAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAg                                                                                                    <  2:1621767/78‑1 (MQ=255)

                                                                                             cgcAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGTTCCTGCCACCAATGTACTGATTGAAGGCAGTATTGa                                                                                              <  1:160310/79‑1 (MQ=255)

                                                                                             cgcAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGTTCCTGCCACCAATGTACTGATTGAAGGCAGTATTGa                                                                                              >  2:160310/1‑79 (MQ=255)

                                                                                             cgcAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCt                                                                                                                              >  1:489676/1‑47 (MQ=255)

                                                                                             cgcAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCt                                                                                                                              <  2:489676/47‑1 (MQ=255)

                                                                                              gcAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAGTATTGATAACGATCGCGTTACGCTGACTAACCTGGGTGCCGACATCGCCCGCGGGACATTAACCGGa                                 <  1:857283/139‑1 (MQ=255)

                                                                                               cAGATTCGGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAgg                                                                                                       <  2:1077246/68‑1 (MQ=255)

                                                                                               cAGATTCGGTTTAGTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATGGAAgg                                                                                                       >  1:1077246/1‑68 (MQ=255)

                                                                                               cAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGTTCTTGCCACCAATGTAc                                                                                                                 <  2:1204573/58‑1 (MQ=255)

                                                                                               cAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGTTCCTGCCACCAATGTAc                                                                                                                 >  1:1204573/1‑58 (MQ=255)

                                                                                                            gTGCCGGATCGCTTTCGCTCAATGATGCTCCTGccacc                                                                                                                        <  2:1503240/38‑1 (MQ=255)

                                                                                                            gTGCCGGATCGCTTTCGCTCAATGATGCTCCTGccacc                                                                                                                        >  1:1503240/1‑38 (MQ=255)

                                                                                                            gTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAGTa                                                                                                  >  2:554891/1‑60 (MQ=255)

                                                                                                            gTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAGTa                                                                                                  <  1:554891/60‑1 (MQ=255)

                                                                                                            gTGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAGTATTGATAACGATCGCGTTACGCTGACTAACCTGGGTGCCGACATCGCCCGCGGGACATTAACCGGAAACGCGCAGCGTaa                   >  2:146396/1‑139 (MQ=255)

                                                                                                             tGCCGGATCGCTTTCGCTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAGTATTGATAACGATCGCGTTACGCTGACTAACCTGGGTGCCGACATCGCCCGCGGGACATTAACCGGAAACGCGCAGCGTAAc                  >  1:1528018/1‑139 (MQ=255)

                                                                                                                             cTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAGTATTGATAACGATCGCGTTACGCTGACTAACCTGGGTGCCGACATCGCCcgc                                                <  2:399450/93‑1 (MQ=255)

                                                                                                                             cTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAGTATTGATAACGATCGCGTTACGCTGACTAACCTGGGTGCCGACATCGCCcgc                                                >  1:399450/1‑93 (MQ=255)

                                                                                                                             cTCAATGATGCTCCTGCCACCAATGTACTGATTGAAGGCAGTATTGATAACGATCGCGTTACGCTGACTAACCTGGGTGCCGACATCGCCCGCGGGACATTAACCGGAAACGCGCAGCGTAACGCCGACGGCAGCTGGc  <  2:53025/139‑1 (MQ=255)

GCCCGAATAGCGAATGGAAACTGAGCGCGCAGCGGGTAAATGGCGGCGTAGTTCCGTGGTCACCAAAAGCCGGTAAAGTGCTGGGTACGAAGGCGCAGATTCAGTTTAGTGCCGGATCGCTTTCGCTCAATGATGTTCCTGCCACCAATGTACTGATTGAAGGCAGTATTGATAACGATCGCGTTACGCTGACTAACCTGGGTGCCGACATCGCCCGCGGGACATTAACCGGAAACGCGCAGCGTAACGCCGACGGCAGCTGGC  >  NC_000913/3830854‑3831117

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 27 ≤` `ATCG/ATCG` `< 34 ≤` `ATCG/ATCG` `< 38 ≤` `ATCG/ATCG` `< 40 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A