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
A2 F1 I0 R1 4577 57.4 3436498 77.7% 2670158 63.4

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA minE 1,707,075 A→G 24.2% S100S (AGT→AGC)  yphB ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,707,0750AG24.2% 154.5 / 43.9 125S100S (AGT→AGC) yphBconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (40/54);  new base G (23/7);  total (64/61)
Fisher's exact test for biased strand distribution p-value = 1.47e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 1.00e+00

Only 100 of 141 total aligned reads displayed.

TTACCCGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAGTGCGCATC  >  minE/1707026‑1707143
                                                 |                                                                    
ttACCCGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCgag                                                    <  1:3172951/68‑1 (MQ=255)
ttACCCGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCgag                                                    <  1:613446/68‑1 (MQ=255)
ttACCCGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCgag                                                    <  1:3042404/68‑1 (MQ=255)
ttACCCGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCgag                                                    <  1:2078093/68‑1 (MQ=255)
ttACCCGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCgag                                                    <  1:1185779/68‑1 (MQ=255)
ttACCCGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCgag                                                    <  1:1209724/68‑1 (MQ=255)
ttACCCGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCgag                                                    <  1:1262358/68‑1 (MQ=255)
ttACCCGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCgag                                                    <  1:46744/68‑1 (MQ=255)
    ccGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGacac                                                <  1:641449/68‑1 (MQ=255)
    ccGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGacac                                                <  1:588679/68‑1 (MQ=255)
    ccGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGacac                                                <  1:2335742/68‑1 (MQ=255)
    ccGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGacac                                                <  1:2504919/68‑1 (MQ=255)
    ccGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGacac                                                <  1:437108/68‑1 (MQ=255)
    ccGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGacac                                                <  1:3293655/68‑1 (MQ=255)
     cGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGAcaca                                               <  1:2525517/68‑1 (MQ=255)
     cGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGAcaca                                               <  1:2644411/68‑1 (MQ=255)
     cGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGAcaca                                               <  1:2958422/68‑1 (MQ=255)
     cGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGAcaca                                               <  1:1882088/68‑1 (MQ=255)
     cGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGAcaca                                               <  1:1836660/68‑1 (MQ=255)
     cGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGAcaca                                               <  1:3078880/68‑1 (MQ=255)
     cGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGAcaca                                               <  1:1003143/68‑1 (MQ=255)
     cGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGAcaca                                               <  1:700534/68‑1 (MQ=255)
     cGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGAcaca                                               <  1:679054/68‑1 (MQ=255)
      gATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGAcaca                                               <  1:1919366/67‑1 (MQ=255)
        tAGTGATAAACACCGCTGAGATGTTCATACACCAGACACAAGCTATCATCGCTGCGCGAGACACATTGc                                           <  1:507764/69‑1 (MQ=255)
        tAGTGATAAACACCGCTGAGATGTTCATACACCAGACACAAGCTATCATCGCTGCGCGAGACACATTGc                                           <  1:2231454/69‑1 (MQ=255)
               aGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCg                                     <  1:1664555/68‑1 (MQ=255)
               aGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCg                                     <  1:2865798/68‑1 (MQ=255)
               aGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCg                                     <  1:3345398/68‑1 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:2869830/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:871035/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:1112239/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:368392/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:272944/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:3349733/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:1785264/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:2500704/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:1707165/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:2414976/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:966177/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:2331494/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:50941/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:1626135/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:2220828/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:1119431/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:2996514/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:2114927/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCcca                                 >  1:2091840/1‑67 (MQ=255)
                    ccGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTCCGAGACACATTGCCACTCGCcca                                 >  1:1765849/1‑67 (MQ=255)
                     cGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGGGCGAGAcaca                                               <  1:160136/52‑1 (MQ=255)
                      gCTGCGATGTTCATACACCAGACACAAACTATCATCGCtgt                                                         >  1:2530992/1‑41 (MQ=255)
                      gCTGCGATGTTCATACACCAGACACAAACTATCATCGCtgt                                                         >  1:2929578/1‑41 (MQ=255)
                      gCTGCGATGTTCATACACCAGACACAAACTATCATCGCtgt                                                         >  1:2702372/1‑41 (MQ=255)
                      gCTGCGATGTTCATACACCAGACACAAACTATCATCGCtgt                                                         >  1:3259605/1‑41 (MQ=255)
                      gCTGCGATGTTCATACACCAGACACAAACTATCATCGCtgt                                                         >  1:344522/1‑41 (MQ=255)
                      gCTGCGATGTTCATACACCAGACACAAACTATCATCGCtgt                                                         >  1:1965604/1‑41 (MQ=255)
                      gCTGCGATGTTCATACACCAGACACAAACTATCATCGCtgt                                                         >  1:1328951/1‑41 (MQ=255)
                      gCTGCGATGTTCATACACCAGACACAAACTATCATCGCtgt                                                         >  1:1466124/1‑41 (MQ=255)
                      gCTGCGATGTTCATACACCAGACACAAACTATCATCGCtgt                                                         >  1:1638175/1‑41 (MQ=255)
                      gCTGCGATGTTCATACACCAGACACAAACTATCATCGCtgt                                                         >  1:2145725/1‑41 (MQ=255)
                      gCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGAcaca                                               <  1:2977791/51‑1 (MQ=255)
                                    acacCAGACACAAGCTATCATCGCTGCGCGAGACACATTGCCACTCGc                                    >  1:761119/1‑48 (MQ=38)
                                    acacCAGACACAAGCTATCATCGCTGCGCGAGACACATTGCCACTCGCCCAACCAGCCATCGcc                    >  1:1240862/1‑64 (MQ=255)
                                    acacCAGACACAAGCTATCATCGCTGCGCGAGACACATTGCCACTCGCCCAACCAGCCATCGcc                    >  1:2128303/1‑64 (MQ=255)
                                    acacCAGACACAAGCTATCATCGCTGCGCGAGACACATTGCCACTCGCCCAACCAGCCATCGCCg                   >  1:431721/1‑65 (MQ=255)
                                    acacCAGACACAAGCTATCATCGCTGCGCGAGACACATTGCCACTCGCCCAACCAGCCATCGCCg                   >  1:3199790/1‑65 (MQ=255)
                                    acacCAGACACAAGCTATCATCGCTGCGCGAGACACATTGCCACTCGCCCAACCAGCCATCGCCg                   >  1:257763/1‑65 (MQ=255)
                                    acacCAGACACAAGCTATCATCGCTGCGCGAGACACATTGCCACTCGCCCAACCAGCCATCGCCg                   >  1:3408903/1‑65 (MQ=255)
                                    acacCAGACACAAGCTATCATCGCTGCGCGAGACACATTGCCACTCGCCCAACCAGCCATCGCCg                   >  1:479002/1‑65 (MQ=255)
                                    acacCAGACACAAGCTATCATCGCTGCGCGAGACACATTGCCACTCGCCCAACCAGCCATCGCCg                   >  1:589254/1‑65 (MQ=255)
                                    acacCAGACACAAGCTATCATCGCTGCGCGAGACACATTGCCACTCGCCCAACCAGCCATCGCCg                   >  1:650320/1‑65 (MQ=255)
                                    acacCAGACACAAGCTATCATCGCTGCGCGAGACACATTGCCACTCGCCCAACCAGCCATCGCCg                   >  1:2780625/1‑65 (MQ=255)
                                    acacCAGACACAAGCTATCATCGCTGCGCGAGACACATTGCCACTCGCCCAACCAGCCATCGCCg                   >  1:2633283/1‑65 (MQ=255)
                                    acacCAGACACAAGCTATCATCGCTGCGCGAGACACATTGCCACTCGCCCAACCAGCCATCGCCg                   >  1:1842155/1‑65 (MQ=255)
                                    acacCAGACACAAGCTATCATCGCTGCGCGAGACACATTGCCACTCGCCCAACCAGCCATCGCCg                   >  1:2542964/1‑65 (MQ=255)
                                    acacCAGACACAAGCTATCATCGATGCGCGAGACACATTGCCACTCGCCCAACCAGCCATCGCCg                   >  1:1731422/1‑65 (MQ=255)
                                    acacCAGACACAACCTATCATCGCTGCGAGAGaca                                                 >  1:2686464/1‑35 (MQ=25)
                                    aaacCAGACACAAGCTATCATCGCTGCGCGAGACACATTGCCACTCGCCCAACCAGCCATCGCCg                   >  1:358920/3‑65 (MQ=255)
                                         aGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCCCATCCAGCCATCGCCGTGTAGATAg          <  1:864330/69‑1 (MQ=255)
                                         aGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAg          <  1:2371947/69‑1 (MQ=255)
                                         aGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAg          <  1:972974/69‑1 (MQ=255)
                                         aGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAg          <  1:1512909/69‑1 (MQ=255)
                                         aGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAg          <  1:2223151/69‑1 (MQ=255)
                                         aGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAg          <  1:2272111/69‑1 (MQ=255)
                                         aGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAg          <  1:2275691/69‑1 (MQ=255)
                                         aGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAg          <  1:476668/69‑1 (MQ=255)
                                         aGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAg          <  1:401098/69‑1 (MQ=255)
                                         aGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAg          <  1:262821/69‑1 (MQ=255)
                                         aGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAg          <  1:2966859/69‑1 (MQ=255)
                                                aaCTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCGTCGCCGTGTAGATAGTGCGCAt   >  1:2809766/1‑69 (MQ=255)
                                                aaCTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAGTGCGCAt   >  1:247377/1‑69 (MQ=255)
                                                aaCTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAGTGCGCAt   >  1:1001229/1‑69 (MQ=255)
                                                aaCTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAGTGCGCAt   >  1:1702347/1‑69 (MQ=255)
                                                aaCTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAGTGCGCAt   >  1:1009052/1‑69 (MQ=255)
                                                 aCTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAGTGCGCATc  <  1:3161365/69‑1 (MQ=255)
                                                 aCTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAGTGCGCATc  <  1:16213/69‑1 (MQ=255)
                                                 aCTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAGTGCGCATc  <  1:1430342/69‑1 (MQ=255)
                                                 aCTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAGTGCGCATc  <  1:1426023/69‑1 (MQ=255)
                                                 aCTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAGTGCGCATc  <  1:1290987/69‑1 (MQ=255)
                                                 aCTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAGTGCGCATc  <  1:3008822/69‑1 (MQ=255)
                                                 |                                                                    
TTACCCGATAGTGATAGACACCGCTGCGATGTTCATACACCAGACACAAACTATCATCGCTGTGCGAGACACATTGCCACTCGCCCAGCCAGCCATCGCCGTGTAGATAGTGCGCATC  >  minE/1707026‑1707143

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 21 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A