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
A6 F21 I0 R1	2169	63.0	3952800	76.2%	3012033	62.4

Breseq alignment

BRESEQ :: Evidence

Predicted mutation
evidence	seq id	position	mutation	freq	annotation	gene	description
RA	minE	1,440,227	G→A	9.0%	Y25Y (TAC→TAT)	ompC ←	outer membrane porin protein C

Read alignment evidence...
	seq id	position		ref	new	freq	score (cons/poly)	reads	annotation	genes	product
*	minE	1,440,227	0	G	A	9.0%	202.5 / 7.4	68	Y25Y (TAC→TAT)	ompC	outer membrane porin protein C
Reads supporting (aligned to +/- strand): ref base G (34/27); new base A (2/4); total (37/31)
Fisher's exact test for biased strand distribution p-value = 4.04e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.74e-01

CTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGACCAGGAGGGACAGTACTTTAACT  >  minE/1440157‑1440296

cTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTttgttg                                                                       >  1:3943264/1‑71 (MQ=255)

 tttGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTttgttg                                                                       >  1:1547661/1‑70 (MQ=255)

   tgttgtCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTttgttg                                                                       <  1:3432314/68‑1 (MQ=255)

   tgttgtCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTa                                                                     >  1:1210375/1‑70 (MQ=255)

   tgttgtCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTa                                                                     <  1:3012564/70‑1 (MQ=255)

   tgttgtCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTa                                                                     >  1:2385075/1‑70 (MQ=255)

     ttgtCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAAc                                                                  <  1:2813360/71‑1 (MQ=255)

     ttgtCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAAc                                                                  >  1:2581807/1‑71 (MQ=255)

     ttgtCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAAc                                                                  <  1:424806/71‑1 (MQ=255)

     ttgtCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAAc                                                                  <  1:353164/71‑1 (MQ=255)

      tgtCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACt                                                                 >  1:510970/1‑71 (MQ=255)

       gtCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACt                                                                 <  1:470833/70‑1 (MQ=255)

        tCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTc                                                               <  1:3081382/71‑1 (MQ=255)

          agagAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTcag                                                             >  1:2384350/1‑71 (MQ=255)

          agagAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTcag                                                             <  1:3441387/71‑1 (MQ=255)

          agaaAAATAATGCAGGCCATCAACTTTGCCATACAGATCTAATTTGTTGCCGTCTTTATTATAAACTTcgg                                                             <  1:2663954/71‑3 (MQ=9)

              aaaTAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTa                                                                     >  1:2676410/1‑59 (MQ=255)

               aaTAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCg                                                        <  1:1566089/71‑1 (MQ=255)

                aTAGTGAAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTaaa                                                                   >  1:510515/1‑59 (MQ=255)

                 tAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGtt                                                      >  1:2540822/1‑71 (MQ=255)

                   gtccAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGttt                                                     <  1:2142652/67‑1 (MQ=255)

                   gTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGttt                                                     <  1:1046119/70‑1 (MQ=255)

                   gTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGttt                                                     <  1:3622522/70‑1 (MQ=255)

                   gTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGttt                                                     <  1:1923652/70‑1 (MQ=255)

                   gTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTtg                                                    <  1:1767317/71‑1 (MQ=255)

                       aGGCCATCAACTTTGCCATACAGATCTAATTTGTTGCCGTCTTTATTATAAACTTCGGCTGCATGtgcag                                                 <  1:563832/70‑3 (MQ=12)

                        ggCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTtg                                                    <  1:476000/66‑1 (MQ=255)

                         gCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTtgttgt                                                                      <  1:923438/47‑1 (MQ=255)

                           cGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCt                                            >  1:2511712/1‑71 (MQ=255)

                             tCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGc                                          <  1:3700968/71‑1 (MQ=255)

                              cTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGc                                          >  1:3220835/1‑70 (MQ=255)

                               tACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTa                                                                     >  1:1964943/1‑42 (MQ=255)

                               tACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTtgctgc                                                >  1:1141268/1‑63 (MQ=255)

                               tACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTtgctgc                                                >  1:3232651/1‑63 (MQ=255)

                               tACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTtgctgc                                                >  1:2443296/1‑63 (MQ=255)

                                aCTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTaaa                                                                   >  1:1361547/1‑43 (MQ=255)

                                 cTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTtg                                                    >  1:3695843/1‑57 (MQ=255)

                                  tttACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGc                                          >  1:1568550/1‑66 (MQ=255)

                                   ttACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACtt                                                                >  1:3695358/1‑43 (MQ=255)

                                    tACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACca                                     <  1:3271827/69‑1 (MQ=255)

                                    tACCGTACAGATCTAATTTGTTGCCGTCTTTGTTCTaa                                                                    >  1:3523863/1‑38 (MQ=255)

                                       cGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACcagca                                  >  1:31472/1‑69 (MQ=255)

                                         tACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGc                              <  1:3365432/71‑1 (MQ=255)

                                         tACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGc                              <  1:3335980/71‑1 (MQ=255)

                                          aCAGATCTAATTTGTTGCCGTCTTTATTATAAACTTCGGCTGCATGtgcagc                                                <  1:135513/52‑1 (MQ=16)

                                          aCAGATCTAATTTGTTGCCGTCTTTATTATAAACTTCGGCTGCATGTGCAGCACCTGCGGCgagcaggg                               >  1:2582446/1‑67 (MQ=255)

                                           cAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCt                             <  1:3209872/70‑1 (MQ=255)

                                           cAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTg                            >  1:154628/1‑71 (MQ=255)

                                           cAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTg                            <  1:1699741/71‑1 (MQ=255)

                                            aGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCt                             <  1:1511783/69‑1 (MQ=255)

                                            aGATCTAATTTGTTGCCGTCTTTATTATAAACTTCGGCTGCATGTGCAGCACCTGCGGCGAgcagggcagg                           <  1:735141/71‑1 (MQ=255)

                                              aTCTAATTTGTTGCCGTCTTTGTTGTAAACTTcagca                                                           <  1:958681/37‑1 (MQ=255)

                                              aTCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGa                         >  1:1703399/1‑71 (MQ=255)

                                              aTCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGa                         >  1:3899087/1‑71 (MQ=255)

                                               tCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGAc                        >  1:1112491/1‑71 (MQ=255)

                                               tCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGAc                        >  1:2645839/1‑71 (MQ=255)

                                                cTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGAc                        >  1:3276002/1‑70 (MQ=255)

                                                cTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGAc                        >  1:2993910/1‑70 (MQ=255)

                                                  aaTTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGACCag                     >  1:2720678/1‑71 (MQ=255)

                                                   aTTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACcagcag                                 >  1:1453407/1‑58 (MQ=255)

                                                   aTTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGa                         <  1:711962/66‑1 (MQ=255)

                                                   aTTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGACCagg                    <  1:669712/71‑1 (MQ=255)

                                                   aTTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGACCag                     >  1:2489047/1‑70 (MQ=255)

                                                   aTTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGACCag                     >  1:333375/1‑70 (MQ=255)

                                                   aTTTGTTGCCGTCTTTATTATAAACTTCGGCTGCATGTGCAGCACCTg                                           >  1:3165087/1‑48 (MQ=12)

                                                    tttGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGACCagga                   <  1:2817526/71‑1 (MQ=255)

                                                    tttGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGACCagga                   <  1:3751257/71‑1 (MQ=255)

                                                      tgttgCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGACCaggagg                 >  1:3042709/1‑71 (MQ=255)

                                                        ttgCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTa                                        >  1:2374682/1‑46 (MQ=255)

                                                          gCCGTCTTTGTTGTAAACTTCAGCAGCGTTtgctgc                                                >  1:2959110/1‑36 (MQ=255)

                                                            cGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTgg                           <  1:3276464/55‑1 (MQ=255)

                                                              tCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGACCAGGAGGGACAGTAc         >  1:420652/1‑71 (MQ=255)

                                                                  tgttgtAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGACCAGGAGGGACAGTACttt      <  1:349458/70‑1 (MQ=255)

                                                                  tgttgtAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGACCAGGAGGGACAGTACttt      >  1:1298770/1‑70 (MQ=255)

                                                                  tgttgtAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGACCAGGAGGGACAGTACt        <  1:3597181/68‑1 (MQ=255)

                                                                   gttgtAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGACCAGGAGGGACAGTACTTTaa    >  1:277056/1‑71 (MQ=255)

                                                                   gttgtAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGACCAGGAGGGACAGTACTTTaa    >  1:2999125/1‑71 (MQ=255)

                                                                     tgtAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGACCAGGAGGGACAGTACTTTaa    <  1:2823685/69‑1 (MQ=255)

                                                                     tgtAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGACCAGGAGGGACAGTACTTTAACt  >  1:881125/1‑71 (MQ=255)

CTTTGTTGTCAGAGAAATAGTGCAGGCCGTCTACTTTACCGTACAGATCTAATTTGTTGCCGTCTTTGTTGTAAACTTCAGCAGCGTTTGCTGCGCCTGCTACCAGCAGAGCTGGGACCAGGAGGGACAGTACTTTAACT  >  minE/1440157‑1440296

Alignment Legend
Aligned base mismatch/match (shaded by quality score): `ATCG/ATCG` `< 3 ≤` `ATCG/ATCG` `< 14 ≤` `ATCG/ATCG` `< 32 ≤` `ATCG/ATCG` `< 36 ≤` `ATCG/ATCG`
Unaligned base: `atcg` Masked matching base: `atcg` Alignment gap: `‑` Deleted base: `‑`

GATK/CNVnator alignment

N/A