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 1,353,786 A→T 20.4% R74R (CGT→CGA)  yohL ← conserved hypothetical protein

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*minE1,353,7860AT20.4% 160.7 / 34.6 88R74R (CGT→CGA) yohLconserved hypothetical protein
Reads supporting (aligned to +/- strand):  ref base A (28/42);  new base T (9/9);  total (37/51)
Fisher's exact test for biased strand distribution p-value = 5.93e-01
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.06e-01

AATAAATTATTTGATATATGAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCACTTCCCGCATCA  >  minE/1353729‑1353853
                                                         |                                                                   
aataaATTATTTGATATATGAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTc                                                          <  1:2153139/69‑1 (MQ=255)
aataaATTATTTGATATATGAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTc                                                          <  1:1459794/69‑1 (MQ=255)
aataaATTATTTGATATATGAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTc                                                          <  1:1267246/69‑1 (MQ=255)
  taaATTATTTGATATATGAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCa                                                         <  1:2905372/68‑1 (MQ=255)
  taaATTATTTGATATATGAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCa                                                         <  1:2126368/68‑1 (MQ=255)
  taaATTATTTGATATATGAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCa                                                         <  1:3246008/68‑1 (MQ=255)
  taaATTATTTGATATATGAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCa                                                         <  1:1623222/68‑1 (MQ=255)
  taaATTATTTGATATATGAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCa                                                         <  1:1151030/68‑1 (MQ=255)
  taaATTATTTGATATATGAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCa                                                         <  1:303833/68‑1 (MQ=255)
  taaATTATTTGATATATGAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCa                                                         <  1:2458983/68‑1 (MQ=255)
             atatatGAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTg                                              <  1:2422722/68‑1 (MQ=255)
             atatatGAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTg                                              <  1:3293923/68‑1 (MQ=255)
             atatatGAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTg                                              <  1:757677/68‑1 (MQ=255)
             atatatGAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTg                                              <  1:816235/68‑1 (MQ=255)
                taagAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCTCGTTTTAGCTCATCCCCCTGGTGAACg                                          <  1:1281511/66‑1 (MQ=255)
                taagAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCTCGTTTTAGCTCATCCCCCTGGTGAACg                                          <  1:1420493/66‑1 (MQ=255)
                taagAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCTCGTTTTAGCTCATCCCCCTGGTGAACg                                          <  1:1154752/66‑1 (MQ=255)
                taagAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCTCGTTTTAGCTCATCCCCCTGGTGAACg                                          <  1:1517350/66‑1 (MQ=255)
                taagAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCTCGTTTTAGCTCATCCCCCTGGTGAACg                                          <  1:2139399/66‑1 (MQ=255)
                taagAATCCAGCACCTTCAGAAAGACATCCAGATCTTCTTCTCGTTTTAGCTCATCCCCCTGGTGAACg                                          <  1:1002490/66‑1 (MQ=255)
                 aagAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCTCGTTTTAGCTCATCCCCCTGGTGAACg                                          <  1:3025708/66‑1 (MQ=255)
                  tGAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGAt                                        >  1:2935795/1‑69 (MQ=255)
                  agAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCTCGTTTTAGCTCATCCCCCTGGTGAACg                                          <  1:2935672/66‑1 (MQ=255)
                     aTCCAGCACCTTCAGAACGACATCCAGATCTTCTTCTCGtttt                                                               >  1:3087459/1‑43 (MQ=255)
                     aTCCAGCACCTTCAGAACGACATCCAGATCTTCTTCTCGTTTTAGCTCATCCCCCTGGTGAACGAtgtg                                     >  1:1002510/1‑69 (MQ=255)
                     aTCCAGCACCTTCAGAACGACATCCAGATCTTCTTCTCGTTTTAGCTCATCCCCCTGGTGAACGAtgtg                                     >  1:3036380/1‑69 (MQ=255)
                     aTCCAGCACCTTCAGAACGACATCCAGATCTTCTTCTCGTTTTAGCTCATCCCCCTGGTGAACGAtgtg                                     >  1:107886/1‑69 (MQ=255)
                     aTCCAGCACCTTCAGAACGACATCCAGATCTTCTTCTCGTTTTAGCTCATCCCCCTGGTGAACGAtgtg                                     >  1:1889390/1‑69 (MQ=255)
                     aTCCAGCACCTTCAGAACGACATCCAGATCTTCTTCTCGTTTTAGCTCATCCCCCTGGTGAACGAtgtg                                     >  1:74426/1‑69 (MQ=255)
                     aTCCAGCACCTTCAGAACGACATCCAGATCTTCTTCTCGTTTTAGCTCATCCCCCTGGTGAACGAtgtg                                     >  1:690393/1‑69 (MQ=255)
                     aTCCAGCACCTTCAGAACGACATCCAGATCTTCTTCTCGTTTTAGCTCATCCCCCTGGTGAACGAtgtg                                     >  1:3246323/1‑69 (MQ=255)
                     aTCCAGCACCTTCAGAACGACATCCAGATCTTCTTCTCGTTTTAGCTCATACCCCTGGTGAACGAtgtg                                     >  1:2020106/1‑69 (MQ=255)
                      tCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATgtgt                                    <  1:2734531/69‑1 (MQ=255)
                      tCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATgtgt                                    <  1:2395657/69‑1 (MQ=255)
                      tCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATgtgt                                    <  1:23557/69‑1 (MQ=255)
                      tCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATgtgt                                    <  1:2340717/69‑1 (MQ=255)
                             ccTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTcc                                 >  1:2653601/1‑65 (MQ=255)
                             ccTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTcc                                 >  1:3133813/1‑65 (MQ=255)
                             ccTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTcc                                 >  1:1950860/1‑65 (MQ=255)
                               ttCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAg                            >  1:2236299/1‑68 (MQ=255)
                               ttCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAg                            >  1:2348053/1‑68 (MQ=255)
                               ttCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAg                            >  1:1564898/1‑68 (MQ=255)
                               ttCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAg                            >  1:1426472/1‑68 (MQ=255)
                               ttCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAg                            >  1:4248/1‑68 (MQ=255)
                               ttCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAg                            >  1:2537768/1‑68 (MQ=255)
                               ttCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAg                            >  1:3169186/1‑68 (MQ=255)
                               ttCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAg                            >  1:306525/1‑68 (MQ=255)
                               ttCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAg                            >  1:791958/1‑68 (MQ=255)
                                 cAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATc                                                       <  1:323323/39‑1 (MQ=255)
                                 cAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATc                                                       <  1:3415199/39‑1 (MQ=255)
                                 cAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATc                                                       <  1:2565118/39‑1 (MQ=255)
                                 cAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATc                                                       <  1:2036273/39‑1 (MQ=255)
                                 cAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATc                                                       <  1:111795/39‑1 (MQ=255)
                                 cAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATc                                                       <  1:1137905/39‑1 (MQ=255)
                                 cAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATc                                                       <  1:2370973/39‑1 (MQ=255)
                                 cAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATc                                                       <  1:2126252/39‑1 (MQ=255)
                                    aaCGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGAc                       <  1:1204897/68‑1 (MQ=255)
                                     aCGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGAcc                      >  1:2748016/1‑68 (MQ=255)
                                     aCGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGAcc                      >  1:3386984/1‑68 (MQ=255)
                                     aCGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGAcc                      >  1:3393383/1‑68 (MQ=255)
                                     aCGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGAcc                      >  1:1405144/1‑68 (MQ=255)
                                     aCGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGAcc                      >  1:2098943/1‑68 (MQ=255)
                                     aCGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGAcc                      >  1:1353909/1‑68 (MQ=255)
                                     aCGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGAcc                      >  1:1233540/1‑68 (MQ=255)
                                     aCGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGAcc                      >  1:830876/1‑68 (MQ=255)
                                     aCGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGAcc                      >  1:2705088/1‑68 (MQ=255)
                                          aTCCAGATCTTCTTCTCGTTTTAGCTCATCCCCCTGGTGAACg                                          <  1:612100/43‑1 (MQ=255)
                                            ccAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCa              <  1:428568/69‑1 (MQ=255)
                                            ccAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCa              <  1:1012768/69‑1 (MQ=255)
                                            ccAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCa              <  1:96860/69‑1 (MQ=255)
                                            ccAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCa              <  1:2909845/69‑1 (MQ=255)
                                            ccAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCa              <  1:166025/69‑1 (MQ=255)
                                            ccAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCa              <  1:265927/69‑1 (MQ=255)
                                            ccAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCAGTCAGATGACCTTTAATCa              <  1:2704437/69‑1 (MQ=255)
                                             cAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCa              <  1:3295834/68‑1 (MQ=255)
                                               gATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCACtt           >  1:3180132/1‑69 (MQ=255)
                                               gATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCACtt           >  1:2664506/1‑69 (MQ=255)
                                               gATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCACtt           >  1:307404/1‑69 (MQ=255)
                                                 tcttctTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCACTTcc         >  1:1432851/1‑69 (MQ=255)
                                                  cttcttCACGTTTTAGCTCAACCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCACTTcc         >  1:2764011/1‑68 (MQ=255)
                                                       tcACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCACTTCCCGCa     <  1:2222965/67‑1 (MQ=255)
                                                       tcACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCACTTCCCGCa     <  1:2979418/67‑1 (MQ=255)
                                                       tcACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCACTTCCCGCa     <  1:26552/67‑1 (MQ=255)
                                                       tcACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCACTTCCCGCa     <  1:3127750/67‑1 (MQ=255)
                                                       tcACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCACTTCCCGCa     <  1:1776922/67‑1 (MQ=255)
                                                       tcACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCACTTCCCGCa     <  1:1446374/67‑1 (MQ=255)
                                                       tcACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCACTTCCCGCa     <  1:1646998/67‑1 (MQ=255)
                                                        cACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCACTTCCCGCATCa  >  1:2879856/1‑69 (MQ=255)
                                                         |                                                                   
AATAAATTATTTGATATATGAATCCAGCACCTTCAGAACGACATCCAGATCTTCTTCACGTTTTAGCTCATCCCCCTGGTGAACGATGTGTTCCGTCAGATGACCTTTAATCACTTCCCGCATCA  >  minE/1353729‑1353853

Alignment Legend
Aligned base mismatch/match (shaded by quality score): ATCG/ATCG < 3 ≤ ATCG/ATCG < 27 ≤ ATCG/ATCG < 32 ≤ ATCG/ATCG < 36 ≤ ATCG/ATCG
Unaligned base: atcg    Masked matching base: atcg    Alignment gap: ‑    Deleted base: ‑

GATK/CNVnator alignment

N/A