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
A1 F21 I0 R2 308 27.9 1975068 96.7% 1909890 67.2

Breseq alignment

BRESEQ :: Evidence
Predicted mutation
evidence seq id position mutation freq annotation gene description
RA W3110S.gb 236,107 A→C 45.2% E14A (GAA→GCA)  dnaQ → DNA polymerase III epsilon subunit

Read alignment evidence...
  seq id position ref new freq score (cons/poly) reads annotation genes product
*W3110S.gb236,1070AC45.2% 21.1 / 143.1 82E14A (GAA→GCA) dnaQDNA polymerase III epsilon subunit
Reads supporting (aligned to +/- strand):  ref base A (34/11);  new base C (15/22);  total (49/33)
Fisher's exact test for biased strand distribution p-value = 1.64e-03
Kolmogorov-Smirnov test that lower quality scores support variant p-value = 9.88e-01

TCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAG  >  W3110S.gb/236048‑236162
                                                           |                                                       
tCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTa                                              >  1:785706/1‑71 (MQ=255)
tCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTa                                              >  1:569705/1‑71 (MQ=255)
tCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTa                                              >  1:198771/1‑71 (MQ=255)
             aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTgg                                 >  1:56000/1‑71 (MQ=255)
             aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTgg                                 >  1:469377/1‑71 (MQ=255)
             aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTgg                                 >  1:114240/1‑71 (MQ=255)
             aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTgg                                 >  1:18775/1‑71 (MQ=255)
             aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTgg                                 >  1:1233678/1‑71 (MQ=255)
             aCCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTgg                                 >  1:1317161/1‑71 (MQ=255)
                 cTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTgcg                             <  1:108599/71‑1 (MQ=255)
                 cTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTgcg                             <  1:215100/71‑1 (MQ=255)
                    tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                          <  1:212371/71‑1 (MQ=255)
                    tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                          <  1:1184349/71‑1 (MQ=255)
                    tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                          <  1:259588/71‑1 (MQ=255)
                    tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                          <  1:1767759/71‑1 (MQ=255)
                    tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                          <  1:1338218/71‑1 (MQ=255)
                    tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                          <  1:1380085/71‑1 (MQ=255)
                    tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                          <  1:1384901/71‑1 (MQ=255)
                    tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                          <  1:1422434/71‑1 (MQ=255)
                    tGAGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCAc                          <  1:1450645/71‑1 (MQ=255)
                      aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                        >  1:917295/1‑71 (MQ=255)
                      aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                        >  1:364468/1‑71 (MQ=255)
                      aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                        >  1:1600331/1‑71 (MQ=255)
                      aGCACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTa                        >  1:78417/1‑71 (MQ=255)
                        cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                      <  1:1194498/71‑1 (MQ=255)
                        cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                      <  1:565486/71‑1 (MQ=255)
                        cACTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                      <  1:564691/71‑1 (MQ=255)
                         aCTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                      <  1:1277588/70‑1 (MQ=255)
                         aCTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                      <  1:916897/70‑1 (MQ=255)
                         aCTGCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                      <  1:31338/70‑1 (MQ=255)
                            gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                  >  1:1387294/1‑71 (MQ=255)
                            gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                  >  1:845050/1‑71 (MQ=255)
                            gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                  >  1:1619102/1‑71 (MQ=255)
                            gCAATTACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                  >  1:1883972/1‑71 (MQ=255)
                            gCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                  >  1:1563711/1‑71 (MQ=255)
                            gCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                  >  1:1244682/1‑71 (MQ=255)
                            gCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                  >  1:425724/1‑71 (MQ=255)
                            gCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                  >  1:1835532/1‑71 (MQ=255)
                            gCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                  >  1:458923/1‑71 (MQ=255)
                            gCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                  >  1:595928/1‑71 (MQ=255)
                            gCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAgg                  >  1:671530/1‑71 (MQ=255)
                             cAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                 >  1:362791/1‑71 (MQ=255)
                             cAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGc                 >  1:132070/1‑71 (MQ=255)
                                 tACACGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                      <  1:986546/62‑1 (MQ=255)
                                     cGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAt         <  1:132168/71‑1 (MQ=255)
                                     cGCCAGATCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGAt         <  1:417395/71‑1 (MQ=255)
                                      gCCAGATCTTTCTCGCTACCGCAACGACCGGTATGAACCAGATTGGTGCGCAc                          <  1:452909/53‑1 (MQ=255)
                                         aGATCGTTCTCGATACCGAAACCGCCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt     <  1:130991/71‑1 (MQ=255)
                                         aGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGTCCACAAGATCAtt     <  1:267170/71‑1 (MQ=255)
                                         aGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt     <  1:1264923/71‑1 (MQ=255)
                                         aGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt     <  1:1774830/71‑1 (MQ=255)
                                           aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                      <  1:1660807/52‑1 (MQ=255)
                                           aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                      <  1:799768/52‑1 (MQ=255)
                                           aTCGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATg                      <  1:1025307/52‑1 (MQ=255)
                                           aTCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACt                         >  1:327735/1‑49 (MQ=255)
                                           aTCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt     >  1:1965937/1‑69 (MQ=255)
                                           aTCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt     >  1:208886/1‑69 (MQ=255)
                                           aTCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt     >  1:316880/1‑69 (MQ=255)
                                           aTCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt     >  1:413870/1‑69 (MQ=255)
                                           aTCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga   <  1:158371/71‑1 (MQ=255)
                                           aTCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga   <  1:26443/71‑1 (MQ=255)
                                           aTCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTga   <  1:1254815/71‑1 (MQ=255)
                                           aTCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCAATATGAAGGCCACAAGATCAtt     >  1:1225945/1‑69 (MQ=255)
                                           aTCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGAGCACTATGAAGGCCACAAGATCAtt     >  1:1548931/1‑69 (MQ=255)
                                            tCGTTCTCGATACCTAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTgag  <  1:644373/71‑1 (MQ=255)
                                            tCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTgag  <  1:1136518/71‑1 (MQ=255)
                                             cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                    >  1:765164/1‑52 (MQ=255)
                                             cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                    >  1:49619/1‑52 (MQ=255)
                                             cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                    >  1:573522/1‑52 (MQ=255)
                                             cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                    >  1:1110666/1‑52 (MQ=255)
                                             cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                    >  1:471709/1‑52 (MQ=255)
                                             cGTTCTCGCTACCGCAACCACCGGTATGAACCAGATTGGTGCGCACTATGaa                    >  1:1954546/1‑52 (MQ=255)
                                             cGTTCTCGCTACCGCAACAACCGGTATGAACCAGATTGGTGCGCACTATGaa                    >  1:3631/1‑52 (MQ=255)
                                             cGTTCTCGATACCGAACCCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt     >  1:877359/1‑67 (MQ=255)
                                             cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTgc                              >  1:331438/1‑42 (MQ=255)
                                             cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt     >  1:1607806/1‑67 (MQ=255)
                                             cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt     >  1:1582592/1‑67 (MQ=255)
                                             cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt     >  1:1139912/1‑67 (MQ=255)
                                             cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt     >  1:1878963/1‑67 (MQ=255)
                                             cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt     >  1:1917042/1‑67 (MQ=255)
                                             cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt     >  1:8657/1‑67 (MQ=255)
                                             cGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCAtt     >  1:224122/1‑67 (MQ=255)
                                                           |                                                       
TCTGACATAAATGACCGCTATGAGCACTGCAATTACACGCCAGATCGTTCTCGATACCGAAACCACCGGTATGAACCAGATTGGTGCGCACTATGAAGGCCACAAGATCATTGAG  >  W3110S.gb/236048‑236162

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